YXJO - BACSU - GREMLIN Contacts

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YXJO - Uncharacterized HTH-type transcriptional regulator YxjO

UniProt:	P55181	Sequences: MDLKWLQTFIAAAESESFREAAEHLYLTQPAVSQHMRKLEDELDMRLFLHSGRRVVLTDEGRLFLPYAKEMIHVYQAGKQKVSQWKQGYSRSLTLAVHPYIASYILPRFLPAYIQKHPHVELSTHVAGSDAIKQAVEHNEADIGLSRKDPNTNTLYYQHICEGTLCLAAPFQESRPDAASVLTRYRLLTHDHPSYGDAFLDNIRSHYPYLQMMAVGQTDTAVHMMKAGMGASFLPTYIIKQEEAEKKLMAVSTPAHLELPASQTFMMWKRNSEDIQHFHAMLHDFMQREQV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	291 (276)
Sequences:	79304 (57621)
Seq/√Len:	3468.3

ECOLI - NAC NHAR OXYR YNEJ YEEY CYSB LEUO ABGR LYSR YDHB CYNR YBHD YAHB AAER YFIE CBL TDCA YDCI YNFL ALLS YEIE YAFC YIAU HCAR ILVY YFER YBDO METR TTDR YHAJ DMLR PGRR DSDC XAPR YCAN YHJC GCVA YGFI YBEF YIDZ PERR ICIA YJIE HDFR LRHA
BACSU - YXJO CYSL GLTR YWBI CITR YCGK GLTC YYBE ALSR YWQM YUST YTLI YVBU YOFA BSDA CZCR YRAN YKUM 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_V	3.614	1.00
15_S	24_H	3.374	1.00
158_Q	283_H	2.592	1.00
96_A	141_A	2.508	1.00
67_Y	81_K	2.492	1.00
11_A	24_H	2.396	1.00
173_E	185_Y	2.349	1.00
92_S	123_S	2.214	1.00
225_M	232_S	2.212	1.00
159_H	162_E	2.199	1.00
162_E	263_Q	2.160	1.00
45_M	60_E	2.128	1.00
159_H	263_Q	2.121	1.00
164_T	236_T	2.097	1.00
92_S	121_E	2.066	1.00
8_T	35_H	2.065	1.00
10_I	69_K	2.035	1.00
20_E	23_E	2.022	1.00
67_Y	74_V	2.014	1.00
10_I	14_E	1.977	1.00
178_A	181_V	1.974	1.00
226_K	247_K	1.970	1.00
166_C	236_T	1.969	1.00
112_A	281_M	1.958	1.00
94_T	123_S	1.950	1.00
11_A	15_S	1.943	1.00
162_E	261_A	1.941	1.00
14_E	69_K	1.939	1.00
222_V	242_E	1.938	1.00
10_I	65_L	1.922	1.00
11_A	14_E	1.919	1.00
13_A	57_L	1.882	1.00
226_K	242_E	1.875	1.00
8_T	32_V	1.867	1.00
71_M	75_Y	1.855	1.00
188_L	230_G	1.854	1.00
65_L	69_K	1.815	1.00
169_A	251_V	1.798	1.00
166_C	250_A	1.776	1.00
186_R	212_M	1.746	1.00
49_L	56_V	1.697	1.00
63_L	81_K	1.690	1.00
64_F	78_G	1.683	1.00
18_F	36_M	1.677	1.00
13_A	65_L	1.662	1.00
135_A	140_E	1.642	1.00
157_Y	265_F	1.624	1.00
15_S	20_E	1.619	1.00
10_I	68_A	1.550	1.00
14_E	24_H	1.548	1.00
67_Y	70_E	1.530	1.00
5_W	35_H	1.523	1.00
156_Y	270_R	1.518	1.00
17_S	20_E	1.507	1.00
134_Q	138_H	1.485	1.00
9_F	65_L	1.482	1.00
5_W	42_E	1.481	1.00
5_W	38_K	1.467	1.00
8_T	27_L	1.460	1.00
113_Y	120_V	1.451	1.00
46_R	49_L	1.445	1.00
28_T	31_A	1.443	1.00
88_G	119_H	1.439	1.00
11_A	25_L	1.436	1.00
113_Y	278_F	1.430	1.00
158_Q	268_W	1.424	1.00
19_R	29_Q	1.422	1.00
103_S	219_D	1.418	1.00
174_S	181_V	1.409	1.00
67_Y	77_A	1.407	1.00
197_D	201_D	1.400	1.00
169_A	173_E	1.396	1.00
71_M	78_G	1.379	1.00
51_S	56_V	1.379	1.00
59_D	62_R	1.378	1.00
279_H	283_H	1.373	1.00
156_Y	268_W	1.366	1.00
94_T	125_H	1.365	1.00
136_V	144_G	1.355	1.00
10_I	72_I	1.353	1.00
135_A	141_A	1.339	1.00
90_S	119_H	1.339	1.00
74_V	77_A	1.335	1.00
146_S	267_M	1.328	1.00
64_F	79_K	1.320	1.00
143_I	275_I	1.316	1.00
137_E	154_T	1.312	1.00
171_F	247_K	1.300	1.00
268_W	279_H	1.297	1.00
277_H	280_A	1.296	1.00
163_G	237_Y	1.293	1.00
148_K	265_F	1.287	1.00
116_K	281_M	1.280	1.00
242_E	247_K	1.278	1.00
185_Y	231_A	1.277	1.00
66_P	70_E	1.272	1.00
112_A	116_K	1.269	1.00
198_A	201_D	1.260	1.00
221_A	232_S	1.257	1.00
169_A	231_A	1.251	1.00
67_Y	78_G	1.244	1.00
114_I	212_M	1.235	1.00
3_L	75_Y	1.235	1.00
223_H	226_K	1.234	1.00
171_F	249_M	1.230	1.00
42_E	79_K	1.229	1.00
143_I	266_M	1.222	1.00
27_L	31_A	1.222	1.00
114_I	186_R	1.213	1.00
63_L	66_P	1.205	1.00
266_M	279_H	1.195	1.00
236_T	250_A	1.185	1.00
240_K	244_A	1.178	1.00
111_P	115_Q	1.178	1.00
9_F	48_F	1.177	1.00
159_H	265_F	1.176	1.00
111_P	227_A	1.172	1.00
34_Q	38_K	1.168	1.00
236_T	240_K	1.160	1.00
250_A	253_T	1.150	1.00
9_F	13_A	1.149	1.00
62_R	66_P	1.141	1.00
127_A	135_A	1.134	1.00
37_R	41_D	1.131	1.00
175_R	249_M	1.129	1.00
63_L	67_Y	1.129	1.00
176_P	254_P	1.119	1.00
157_Y	267_M	1.109	1.00
34_Q	37_R	1.105	1.00
123_S	214_A	1.089	1.00
168_A	250_A	1.088	1.00
70_E	77_A	1.086	1.00
177_D	181_V	1.084	1.00
108_R	227_A	1.083	1.00
18_F	55_V	1.079	1.00
102_A	126_V	1.077	1.00
186_R	210_L	1.074	1.00
6_L	68_A	1.073	1.00
112_A	115_Q	1.072	1.00
9_F	47_L	1.071	1.00
33_S	37_R	1.071	1.00
11_A	21_A	1.064	1.00
137_E	152_T	1.052	1.00
223_H	227_A	1.051	1.00
222_V	226_K	1.048	1.00
71_M	74_V	1.047	1.00
204_R	207_Y	1.038	1.00
280_A	283_H	1.038	1.00
117_H	277_H	1.037	1.00
188_L	221_A	1.036	1.00
35_H	38_K	1.029	1.00
12_A	21_A	1.027	1.00
113_Y	281_M	1.023	1.00
215_V	221_A	1.023	1.00
276_Q	280_A	1.022	1.00
170_P	228_G	1.015	1.00
241_Q	245_E	1.011	1.00
79_K	83_S	1.006	1.00
158_Q	279_H	1.003	1.00
4_K	7_Q	0.999	1.00
272_S	275_I	0.988	1.00
125_H	135_A	0.986	1.00
57_L	61_G	0.982	1.00
168_A	239_I	0.981	1.00
64_F	68_A	0.978	1.00
73_H	77_A	0.973	1.00
109_F	282_L	0.973	1.00
7_Q	76_Q	0.973	1.00
113_Y	117_H	0.970	1.00
8_T	25_L	0.963	1.00
12_A	18_F	0.961	1.00
27_L	32_V	0.953	1.00
13_A	48_F	0.950	1.00
76_Q	79_K	0.950	1.00
189_T	211_Q	0.950	1.00
93_L	278_F	0.942	1.00
21_A	32_V	0.939	1.00
164_T	261_A	0.938	1.00
38_K	41_D	0.934	1.00
167_L	231_A	0.930	1.00
281_M	284_D	0.925	1.00
76_Q	80_Q	0.924	1.00
9_F	39_L	0.923	1.00
9_F	57_L	0.917	1.00
215_V	224_M	0.917	1.00
20_E	24_H	0.916	1.00
135_A	138_H	0.912	1.00
179_A	255_A	0.907	1.00
187_L	209_Y	0.903	1.00
96_A	144_G	0.898	1.00
116_K	284_D	0.894	1.00
70_E	73_H	0.892	1.00
48_F	55_V	0.891	1.00
109_F	281_M	0.887	1.00
16_E	56_V	0.887	1.00
99_P	217_Q	0.883	1.00
45_M	82_V	0.880	1.00
242_E	245_E	0.876	1.00
96_A	146_S	0.865	1.00
183_T	207_Y	0.863	1.00
141_A	144_G	0.862	1.00
186_R	211_Q	0.862	1.00
198_A	202_N	0.858	1.00
66_P	69_K	0.855	1.00
133_K	137_E	0.850	1.00
156_Y	159_H	0.849	1.00
75_Y	79_K	0.846	1.00
148_K	263_Q	0.844	1.00
13_A	61_G	0.843	1.00
19_R	23_E	0.839	1.00
25_L	32_V	0.837	1.00
121_E	210_L	0.834	1.00
170_P	173_E	0.834	1.00
95_L	143_I	0.833	1.00
111_P	229_M	0.828	1.00
51_S	54_R	0.826	1.00
173_E	186_R	0.824	1.00
125_H	141_A	0.819	1.00
168_A	232_S	0.809	1.00
29_Q	33_S	0.808	1.00
199_F	203_I	0.808	1.00
13_A	16_E	0.807	1.00
60_E	63_L	0.805	1.00
60_E	82_V	0.805	1.00
77_A	81_K	0.804	1.00
75_Y	78_G	0.803	1.00
63_L	85_W	0.803	1.00
181_V	184_R	0.802	1.00
74_V	78_G	0.801	1.00
9_F	64_F	0.801	1.00
15_S	21_A	0.800	1.00
14_E	65_L	0.796	1.00
16_E	54_R	0.789	1.00
155_L	267_M	0.788	1.00
114_I	229_M	0.787	1.00
201_D	205_S	0.786	1.00
170_P	229_M	0.785	1.00
239_I	242_E	0.785	1.00
164_T	252_S	0.784	1.00
280_A	284_D	0.784	1.00
120_V	274_D	0.781	1.00
180_S	183_T	0.780	1.00
169_A	249_M	0.779	1.00
37_R	46_R	0.778	1.00
16_E	62_R	0.773	1.00
91_R	274_D	0.773	1.00
224_M	229_M	0.766	1.00
178_A	254_P	0.766	1.00
4_K	35_H	0.764	1.00
3_L	72_I	0.763	1.00
273_E	277_H	0.763	1.00
7_Q	11_A	0.761	1.00
12_A	48_F	0.758	1.00
83_S	86_K	0.755	1.00
5_W	8_T	0.755	1.00
12_A	36_M	0.752	1.00
91_R	120_V	0.749	1.00
60_E	85_W	0.742	1.00
49_L	58_T	0.741	1.00
68_A	71_M	0.739	1.00
18_F	32_V	0.739	1.00
12_A	32_V	0.737	1.00
97_V	102_A	0.735	1.00
78_G	82_V	0.735	1.00
69_K	73_H	0.731	1.00
203_I	206_H	0.730	1.00
62_R	65_L	0.726	1.00
201_D	204_R	0.725	1.00
196_G	200_L	0.725	1.00
137_E	155_L	0.725	1.00
200_L	203_I	0.723	1.00
168_A	234_L	0.718	1.00
113_Y	277_H	0.717	1.00
154_T	270_R	0.712	1.00
89_Y	117_H	0.711	1.00
255_A	258_E	0.711	1.00
217_Q	220_T	0.701	1.00
60_E	64_F	0.700	1.00
142_D	275_I	0.698	1.00
235_P	238_I	0.694	1.00
7_Q	10_I	0.694	1.00
116_K	277_H	0.691	1.00
31_A	35_H	0.691	1.00
94_T	141_A	0.689	1.00
59_D	63_L	0.686	1.00
56_V	62_R	0.685	1.00
94_T	142_D	0.679	1.00
57_L	62_R	0.675	1.00
143_I	278_F	0.675	1.00
139_N	269_K	0.673	1.00
191_D	214_A	0.671	1.00
172_Q	228_G	0.670	1.00
277_H	281_M	0.667	1.00
49_L	54_R	0.667	1.00
40_E	45_M	0.665	1.00
64_F	82_V	0.656	1.00
121_E	214_A	0.655	1.00
103_S	223_H	0.654	1.00
67_Y	71_M	0.653	1.00
273_E	276_Q	0.652	1.00
164_T	258_E	0.651	1.00
77_A	80_Q	0.646	1.00
172_Q	249_M	0.643	1.00
190_H	221_A	0.642	1.00
202_N	206_H	0.642	1.00
173_E	177_D	0.641	1.00
23_E	26_Y	0.639	1.00
73_H	76_Q	0.638	1.00
40_E	50_H	0.637	1.00
173_E	231_A	0.637	1.00
108_R	111_P	0.635	1.00
195_Y	198_A	0.635	1.00
187_L	231_A	0.634	1.00
199_F	204_R	0.630	1.00
126_V	216_G	0.627	1.00
178_A	255_A	0.622	1.00
184_R	210_L	0.621	1.00
147_R	262_S	0.621	1.00
167_L	233_F	0.620	1.00
176_P	252_S	0.619	1.00
167_L	182_L	0.616	1.00
199_F	202_N	0.616	1.00
213_M	224_M	0.614	1.00
36_M	40_E	0.614	1.00
278_F	282_L	0.614	1.00
4_K	38_K	0.612	1.00
241_Q	244_A	0.611	1.00
7_Q	72_I	0.611	1.00
12_A	17_S	0.611	1.00
97_V	106_L	0.610	1.00
200_L	204_R	0.606	1.00
21_A	25_L	0.606	1.00
106_L	109_F	0.606	1.00
112_A	284_D	0.605	1.00
80_Q	84_Q	0.604	1.00
68_A	72_I	0.603	1.00
9_F	61_G	0.600	1.00
93_L	274_D	0.600	1.00
93_L	143_I	0.597	1.00
171_F	246_K	0.597	1.00
99_P	128_G	0.586	1.00
191_D	216_G	0.580	1.00
90_S	121_E	0.578	1.00
72_I	76_Q	0.576	1.00
117_H	120_V	0.575	1.00
126_V	217_Q	0.575	1.00
202_N	205_S	0.574	1.00
196_G	201_D	0.573	1.00
63_L	82_V	0.573	1.00
43_L	64_F	0.572	1.00
4_K	8_T	0.571	1.00
18_F	54_R	0.570	1.00
31_A	34_Q	0.567	1.00
45_M	49_L	0.565	1.00
43_L	82_V	0.564	1.00
143_I	279_H	0.563	1.00
28_T	34_Q	0.562	1.00
167_L	187_L	0.561	1.00
221_A	225_M	0.559	1.00
30_P	34_Q	0.558	1.00
197_D	214_A	0.557	1.00
136_V	155_L	0.556	1.00
108_R	112_A	0.554	1.00
215_V	220_T	0.553	1.00
96_A	127_A	0.553	1.00
174_S	177_D	0.553	1.00
165_L	233_F	0.553	1.00
204_R	209_Y	0.551	1.00
48_F	57_L	0.551	1.00
234_L	239_I	0.548	1.00
13_A	62_R	0.545	1.00
96_A	125_H	0.542	1.00
57_L	65_L	0.541	1.00
91_R	119_H	0.541	1.00
101_I	105_I	0.539	1.00
43_L	46_R	0.539	1.00
18_F	29_Q	0.538	1.00
224_M	230_G	0.536	1.00
145_L	282_L	0.535	1.00
148_K	157_Y	0.535	1.00
192_H	214_A	0.533	1.00
46_R	60_E	0.531	1.00
274_D	277_H	0.528	1.00
183_T	208_P	0.528	1.00
8_T	36_M	0.528	1.00
80_Q	83_S	0.526	1.00
16_E	55_V	0.525	1.00
161_C	264_T	0.525	1.00
110_L	122_L	0.525	1.00
105_I	109_F	0.525	1.00
176_P	181_V	0.524	1.00
164_T	259_L	0.522	1.00
268_W	276_Q	0.517	1.00
226_K	245_E	0.515	1.00
97_V	124_T	0.515	1.00
84_Q	89_Y	0.514	1.00
108_R	223_H	0.513	1.00
18_F	50_H	0.512	1.00
252_S	255_A	0.512	1.00
72_I	75_Y	0.511	1.00
275_I	279_H	0.509	1.00
66_P	81_K	0.508	1.00
163_G	262_S	0.508	1.00
218_T	235_P	0.507	1.00
27_L	35_H	0.507	1.00
71_M	79_K	0.506	1.00
136_V	267_M	0.505	1.00
78_G	81_K	0.505	1.00
45_M	86_K	0.505	1.00
156_Y	271_N	0.504	1.00
103_S	217_Q	0.504	1.00
81_K	84_Q	0.503	1.00
8_T	21_A	0.502	1.00
107_P	111_P	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
2h98A	2	0.6804	100	0.115	Contact Map
4x6gA	4	0.9931	100	0.116	Contact Map
3fxqA	3	0.9794	100	0.117	Contact Map
1uthA	2	0.7491	100	0.117	Contact Map
2esnA	3	0.9828	100	0.118	Contact Map
1ixcA	4	0.9759	100	0.118	Contact Map
2h9bA	2	0.6804	100	0.119	Contact Map
1al3A	1	0.6976	100	0.124	Contact Map
3fzvA	4	0.9553	100	0.131	Contact Map
3szpA	3	0.9656	100	0.139	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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