YDFL - BACSU - GREMLIN Contacts

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YDFL - Uncharacterized HTH-type transcriptional regulator YdfL

UniProt:	P96690	Sequences: MKEFFSIGEVSKLFNVKISALRYYDEIGLLKPEYKDEQTNYRYYSTQQFERLDTIKYLRALGLPINKLLDFYNSQNTNTLLHLLKSQQVEIDRKKKELERIERKISRRITHIEDAVNMPLHQISKIKLPAMRVAYLQHEYVLGHDIEHSLAELRTHLNVNEDIFIGKIGLSISAANVKAKQFDKYSSIFMILEDENEKTSSEIIFPSREYLQIRFKGSHPEAEPYYKKLLAYMKEHHYEVAGDSIEITLIDYGITNNLDNYVTEILLPIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	270 (228)
Sequences:	3777 (3199)
Seq/√Len:	211.8

ECOLI - SOXR ZNTR
BACSU - YDFL BMRR BLTR MTA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_Q	106_S	5.102	1.00
95_K	99_E	4.959	1.00
36_D	39_T	3.781	1.00
92_D	102_E	3.221	1.00
87_Q	90_E	3.144	1.00
18_I	22_R	3.046	1.00
45_S	48_Q	2.920	1.00
25_D	31_K	2.873	1.00
30_L	55_I	2.643	1.00
23_Y	27_I	2.459	1.00
51_R	73_N	2.407	1.00
94_K	97_E	2.370	1.00
85_K	113_E	2.311	1.00
95_K	98_L	2.244	1.00
7_I	22_R	2.237	1.00
207_S	211_L	2.221	1.00
36_D	43_Y	2.166	1.00
59_R	65_I	2.152	1.00
33_E	48_Q	2.146	1.00
189_F	192_L	2.119	1.00
215_F	225_Y	2.115	1.00
88_Q	102_E	2.072	1.00
8_G	12_K	2.054	1.00
27_I	65_I	2.028	1.00
64_P	67_K	1.947	1.00
81_L	109_I	1.924	1.00
62_G	94_K	1.918	1.00
88_Q	92_D	1.900	1.00
85_K	109_I	1.809	1.00
211_L	233_M	1.786	1.00
67_K	70_D	1.767	1.00
94_K	98_L	1.752	1.00
91_I	98_L	1.712	1.00
69_L	73_N	1.687	1.00
188_I	192_L	1.663	1.00
10_V	52_L	1.596	1.00
6_S	9_E	1.587	1.00
91_I	102_E	1.586	1.00
88_Q	109_I	1.548	1.00
98_L	102_E	1.527	1.00
95_K	102_E	1.510	1.00
89_V	93_R	1.506	1.00
33_E	45_S	1.495	1.00
28_G	31_K	1.487	1.00
7_I	18_I	1.455	1.00
92_D	106_S	1.448	1.00
81_L	113_E	1.432	1.00
5_F	46_T	1.430	1.00
34_Y	43_Y	1.429	1.00
23_Y	26_E	1.429	1.00
63_L	71_F	1.419	1.00
84_L	105_I	1.409	1.00
127_K	209_E	1.408	1.00
23_Y	65_I	1.398	1.00
187_S	192_L	1.398	1.00
67_K	86_S	1.392	1.00
16_V	52_L	1.387	1.00
211_L	232_Y	1.386	1.00
178_K	181_Q	1.364	1.00
169_G	189_F	1.344	1.00
188_I	193_E	1.344	1.00
56_K	59_R	1.340	1.00
52_L	56_K	1.340	1.00
186_S	189_F	1.334	1.00
174_A	178_K	1.334	1.00
10_V	49_F	1.329	1.00
20_A	23_Y	1.327	1.00
19_S	26_E	1.303	1.00
21_L	25_D	1.301	1.00
114_D	118_M	1.297	1.00
91_I	101_I	1.268	1.00
149_S	152_E	1.266	1.00
51_R	72_Y	1.259	1.00
9_E	12_K	1.256	1.00
169_G	172_I	1.251	1.00
90_E	94_K	1.239	1.00
33_E	47_Q	1.225	1.00
88_Q	105_I	1.218	1.00
175_A	178_K	1.218	1.00
96_K	99_E	1.217	1.00
146_I	150_L	1.209	1.00
109_I	113_E	1.206	1.00
187_S	190_M	1.202	1.00
192_L	196_N	1.202	1.00
174_A	177_V	1.189	1.00
11_S	17_K	1.178	1.00
76_N	79_T	1.175	1.00
130_A	204_I	1.173	1.00
91_I	105_I	1.162	1.00
186_S	192_L	1.158	1.00
35_K	48_Q	1.136	1.00
24_Y	52_L	1.126	1.00
32_P	35_K	1.125	1.00
92_D	95_K	1.119	1.00
39_T	43_Y	1.119	1.00
6_S	43_Y	1.114	1.00
180_K	184_K	1.109	1.00
97_E	101_I	1.105	1.00
127_K	207_S	1.103	1.00
21_L	27_I	1.100	1.00
189_F	196_N	1.099	1.00
162_D	166_G	1.094	1.00
4_F	34_Y	1.091	1.00
31_K	35_K	1.090	1.00
177_V	180_K	1.081	1.00
213_I	225_Y	1.067	1.00
14_F	52_L	1.062	1.00
8_G	18_I	1.054	1.00
90_E	93_R	1.052	1.00
29_L	55_I	1.046	1.00
153_L	157_L	1.041	1.00
156_H	160_N	1.041	1.00
63_L	87_Q	1.040	1.00
89_V	92_D	1.014	1.00
134_A	138_H	1.013	1.00
10_V	48_Q	1.011	1.00
168_I	171_S	1.009	1.00
157_L	160_N	1.004	1.00
35_K	43_Y	0.997	1.00
193_E	197_E	0.996	1.00
193_E	196_N	0.982	1.00
120_L	124_S	0.976	1.00
143_G	147_E	0.975	1.00
150_L	153_L	0.975	1.00
190_M	193_E	0.967	1.00
10_V	14_F	0.961	1.00
169_G	173_S	0.960	1.00
147_E	151_A	0.941	0.99
84_L	109_I	0.936	0.99
25_D	42_R	0.936	0.99
222_A	226_Y	0.936	0.99
180_K	183_D	0.930	0.99
11_S	14_F	0.924	0.99
115_A	118_M	0.923	0.99
106_S	110_T	0.920	0.99
137_Q	183_D	0.917	0.99
176_N	181_Q	0.914	0.99
59_R	62_G	0.909	0.99
130_A	207_S	0.907	0.99
152_E	156_H	0.905	0.99
148_H	151_A	0.891	0.99
125_K	209_E	0.884	0.99
153_L	156_H	0.879	0.99
11_S	18_I	0.873	0.99
81_L	85_K	0.870	0.99
186_S	190_M	0.868	0.99
17_K	23_Y	0.859	0.99
93_R	96_K	0.855	0.99
149_S	157_L	0.852	0.99
213_I	229_L	0.850	0.99
175_A	179_A	0.849	0.99
168_I	172_I	0.848	0.99
149_S	156_H	0.847	0.99
110_T	115_A	0.845	0.99
153_L	161_E	0.843	0.99
121_H	125_K	0.842	0.99
120_L	125_K	0.835	0.99
55_I	68_L	0.834	0.99
192_L	197_E	0.833	0.99
60_A	101_I	0.829	0.99
176_N	180_K	0.828	0.99
177_V	184_K	0.825	0.99
7_I	42_R	0.825	0.99
86_S	89_V	0.820	0.99
18_I	39_T	0.811	0.98
227_K	231_A	0.805	0.98
191_I	196_N	0.798	0.98
189_F	193_E	0.795	0.98
17_K	20_A	0.790	0.98
177_V	181_Q	0.790	0.98
63_L	83_L	0.783	0.98
148_H	152_E	0.782	0.98
178_K	183_D	0.781	0.98
128_L	131_M	0.778	0.98
145_D	148_H	0.777	0.98
215_F	221_E	0.776	0.98
82_H	86_S	0.775	0.98
14_F	30_L	0.775	0.98
179_A	182_F	0.771	0.98
70_D	74_S	0.765	0.98
179_A	184_K	0.763	0.98
186_S	191_I	0.754	0.98
96_K	100_R	0.753	0.97
59_R	68_L	0.752	0.97
198_K	201_S	0.752	0.97
155_T	159_V	0.745	0.97
176_N	184_K	0.743	0.97
174_A	180_K	0.742	0.97
183_D	186_S	0.738	0.97
177_V	182_F	0.737	0.97
78_N	82_H	0.736	0.97
88_Q	91_I	0.736	0.97
67_K	87_Q	0.734	0.97
216_K	228_K	0.732	0.97
7_I	11_S	0.732	0.97
19_S	22_R	0.730	0.97
174_A	184_K	0.729	0.97
156_H	161_E	0.728	0.97
228_K	231_A	0.728	0.97
98_L	101_I	0.727	0.97
43_Y	48_Q	0.727	0.97
181_Q	184_K	0.725	0.97
58_L	71_F	0.724	0.97
184_K	187_S	0.724	0.97
150_L	156_H	0.721	0.97
27_I	59_R	0.717	0.97
192_L	198_K	0.716	0.97
21_L	44_Y	0.715	0.97
209_E	215_F	0.713	0.97
167_K	171_S	0.710	0.96
178_K	182_F	0.710	0.96
152_E	157_L	0.709	0.96
25_D	30_L	0.705	0.96
221_E	224_P	0.701	0.96
127_K	130_A	0.701	0.96
188_I	191_I	0.694	0.96
179_A	183_D	0.691	0.96
60_A	97_E	0.689	0.96
175_A	182_F	0.688	0.96
161_E	165_I	0.687	0.96
133_V	203_I	0.683	0.96
16_V	20_A	0.680	0.95
62_G	97_E	0.679	0.95
135_Y	214_R	0.677	0.95
192_L	195_E	0.677	0.95
133_V	137_Q	0.674	0.95
166_G	169_G	0.672	0.95
30_L	52_L	0.669	0.95
154_R	157_L	0.669	0.95
187_S	191_I	0.666	0.95
165_I	169_G	0.665	0.95
14_F	19_S	0.664	0.95
143_G	146_I	0.662	0.95
195_E	198_K	0.662	0.95
143_G	149_S	0.657	0.95
176_N	182_F	0.656	0.94
145_D	149_S	0.654	0.94
150_L	154_R	0.652	0.94
110_T	114_D	0.649	0.94
53_D	57_Y	0.649	0.94
136_L	140_Y	0.646	0.94
85_K	89_V	0.644	0.94
224_P	227_K	0.640	0.94
14_F	49_F	0.638	0.94
53_D	108_R	0.636	0.94
71_F	83_L	0.635	0.93
70_D	73_N	0.632	0.93
92_D	96_K	0.630	0.93
7_I	25_D	0.629	0.93
10_V	30_L	0.625	0.93
157_L	161_E	0.623	0.93
107_R	111_H	0.619	0.93
184_K	188_I	0.618	0.93
204_I	208_R	0.618	0.93
5_F	140_Y	0.616	0.92
165_I	168_I	0.611	0.92
184_K	189_F	0.611	0.92
21_L	65_I	0.610	0.92
159_V	162_D	0.609	0.92
34_Y	45_S	0.609	0.92
149_S	153_L	0.608	0.92
94_K	101_I	0.605	0.92
63_L	90_E	0.604	0.92
25_D	59_R	0.603	0.92
87_Q	105_I	0.598	0.91
22_R	30_L	0.598	0.91
78_N	116_V	0.597	0.91
166_G	170_L	0.592	0.91
176_N	183_D	0.591	0.91
127_K	131_M	0.590	0.91
174_A	182_F	0.588	0.91
136_L	146_I	0.588	0.91
8_G	11_S	0.587	0.91
220_P	225_Y	0.587	0.91
132_R	136_L	0.585	0.90
186_S	193_E	0.583	0.90
216_K	220_P	0.581	0.90
194_D	197_E	0.580	0.90
38_Q	43_Y	0.577	0.90
201_S	204_I	0.577	0.90
191_I	194_D	0.575	0.90
128_L	133_V	0.575	0.90
48_Q	51_R	0.568	0.89
112_I	116_V	0.565	0.89
147_E	150_L	0.565	0.89
44_Y	68_L	0.565	0.89
208_R	215_F	0.562	0.89
155_T	161_E	0.560	0.88
175_A	181_Q	0.559	0.88
59_R	64_P	0.558	0.88
79_T	82_H	0.558	0.88
87_Q	91_I	0.555	0.88
16_V	98_L	0.554	0.88
20_A	52_L	0.554	0.88
173_S	183_D	0.552	0.88
14_F	25_D	0.552	0.88
44_Y	65_I	0.550	0.88
135_Y	141_V	0.550	0.88
82_H	85_K	0.549	0.87
103_R	106_S	0.548	0.87
29_L	65_I	0.548	0.87
150_L	157_L	0.547	0.87
13_L	41_Y	0.546	0.87
213_I	217_G	0.545	0.87
60_A	94_K	0.543	0.87
19_S	23_Y	0.542	0.87
14_F	108_R	0.540	0.87
165_I	172_I	0.540	0.87
205_F	208_R	0.539	0.86
199_T	202_E	0.538	0.86
184_K	193_E	0.534	0.86
102_E	106_S	0.533	0.86
204_I	209_E	0.532	0.86
77_T	83_L	0.530	0.86
74_S	79_T	0.528	0.85
217_G	221_E	0.526	0.85
85_K	88_Q	0.524	0.85
20_A	65_I	0.523	0.85
111_H	118_M	0.522	0.85
25_D	43_Y	0.521	0.85
71_F	80_L	0.519	0.84
211_L	221_E	0.519	0.84
136_L	139_E	0.518	0.84
8_G	22_R	0.518	0.84
186_S	196_N	0.518	0.84
204_I	207_S	0.517	0.84
87_Q	101_I	0.513	0.84
153_L	172_I	0.513	0.84
189_F	197_E	0.513	0.84
93_R	97_E	0.511	0.83
78_N	206_P	0.511	0.83
180_K	191_I	0.510	0.83
223_E	227_K	0.506	0.83
23_Y	59_R	0.505	0.83
24_Y	207_S	0.504	0.83
154_R	158_N	0.503	0.82
82_H	231_A	0.502	0.82
216_K	227_K	0.502	0.82
189_F	198_K	0.501	0.82
191_I	195_E	0.500	0.82
92_D	99_E	0.500	0.82
112_I	115_A	0.500	0.82

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
1r8eA	2	0.9889	100	0.221	Contact Map
3qaoA	2	0.5111	99.9	0.509	Contact Map
3gpvA	2	0.4111	99.9	0.524	Contact Map
3hh0A	4	0.4889	99.9	0.524	Contact Map
3gp4A	4	0.4704	99.9	0.536	Contact Map
1r8dA	2	0.4037	99.9	0.543	Contact Map
2zhgA	2	0.4444	99.9	0.544	Contact Map
2vz4A	2	0.3704	99.9	0.547	Contact Map
1q06A	2	0.4519	99.9	0.555	Contact Map
4ua1A	2	0.4444	99.9	0.567	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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