YUSO - BACSU - GREMLIN Contacts

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YUSO - Uncharacterized HTH-type transcriptional regulator YusO

UniProt:	O32181	Sequences: MKSADQLMSDIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKAIMARYLSFLTEEEMLQAAHITAKLAQAAETDEKQNMKRGNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	155 (133)
Sequences:	24588 (18142)
Seq/√Len:	1573.2

ECOLI - SLYA MPRA MARR
BACSU - YUSO YCGE YYBA YWHA YFIV MHQR YXAD YPOP YSMB YKOM YWAE YETL YDGG OHRR YDGJ YWOH YDCH YHJH YVMB YVNA YBFA
SULSO - Q97Z53 Q97YG9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_T	96_S	3.240	1.00
51_S	96_S	3.115	1.00
127_E	137_K	2.896	1.00
82_A	96_S	2.690	1.00
53_K	92_V	2.559	1.00
86_N	94_D	2.409	1.00
124_T	127_E	2.395	1.00
130_Q	133_H	2.100	1.00
85_H	93_I	2.074	1.00
39_Q	78_K	2.013	1.00
130_Q	134_I	2.010	1.00
47_K	105_F	1.984	1.00
123_L	134_I	1.880	1.00
53_K	56_E	1.873	1.00
86_N	92_V	1.872	1.00
47_K	97_L	1.815	1.00
127_E	130_Q	1.755	1.00
54_V	72_A	1.724	1.00
122_F	141_A	1.723	1.00
127_E	133_H	1.685	1.00
79_N	100_E	1.621	1.00
72_A	95_L	1.616	1.00
39_Q	74_R	1.607	1.00
14_S	136_A	1.583	1.00
76_E	83_R	1.575	1.00
131_A	134_I	1.525	1.00
49_H	60_R	1.503	1.00
100_E	104_K	1.503	1.00
42_V	71_M	1.500	1.00
73_D	77_Q	1.465	1.00
36_T	39_Q	1.461	1.00
134_I	137_K	1.386	1.00
100_E	103_I	1.379	1.00
104_K	107_E	1.379	1.00
47_K	102_D	1.350	1.00
51_S	84_T	1.338	1.00
51_S	94_D	1.315	1.00
64_K	67_A	1.311	1.00
14_S	139_A	1.287	1.00
45_S	60_R	1.263	1.00
56_E	59_E	1.249	1.00
55_S	65_P	1.248	1.00
42_V	68_V	1.222	1.00
54_V	93_I	1.219	1.00
14_S	132_A	1.214	1.00
33_Q	111_G	1.213	1.00
133_H	137_K	1.198	1.00
33_Q	107_E	1.181	1.00
18_L	139_A	1.173	1.00
55_S	59_E	1.168	1.00
54_V	68_V	1.164	1.00
103_I	107_E	1.162	1.00
73_D	90_R	1.156	1.00
128_M	132_A	1.130	1.00
29_S	111_G	1.124	1.00
66_S	69_T	1.120	1.00
63_V	67_A	1.118	1.00
83_R	93_I	1.116	1.00
32_K	111_G	1.090	1.00
126_E	130_Q	1.081	1.00
17_A	139_A	1.055	1.00
54_V	65_P	1.031	1.00
97_L	101_G	1.020	1.00
73_D	76_E	1.017	1.00
54_V	95_L	1.007	1.00
27_L	31_E	1.002	1.00
99_D	102_D	0.996	1.00
67_A	70_L	0.993	1.00
111_G	114_A	0.993	1.00
38_A	71_M	0.982	1.00
78_K	100_E	0.977	1.00
80_L	104_K	0.959	1.00
123_L	138_L	0.957	1.00
56_E	60_R	0.954	1.00
132_A	136_A	0.950	1.00
127_E	134_I	0.945	1.00
64_K	70_L	0.938	1.00
52_L	56_E	0.936	1.00
99_D	103_I	0.930	1.00
78_K	104_K	0.925	1.00
69_T	73_D	0.921	1.00
85_H	90_R	0.911	1.00
29_S	118_R	0.910	1.00
82_A	98_T	0.907	1.00
18_L	135_T	0.902	1.00
72_A	81_I	0.900	1.00
84_T	94_D	0.897	1.00
49_H	52_L	0.895	1.00
47_K	106_E	0.891	1.00
27_L	37_P	0.888	1.00
63_V	68_V	0.888	1.00
29_S	114_A	0.888	1.00
50_G	102_D	0.886	1.00
52_L	60_R	0.885	1.00
110_A	114_A	0.860	1.00
40_L	108_V	0.858	1.00
102_D	106_E	0.857	1.00
125_E	129_L	0.856	1.00
76_E	82_A	0.850	1.00
16_Q	19_F	0.848	1.00
21_K	139_A	0.845	1.00
86_N	89_D	0.845	1.00
33_Q	108_V	0.835	1.00
70_L	74_R	0.820	1.00
80_L	100_E	0.814	1.00
89_D	92_V	0.810	1.00
116_M	119_Y	0.805	1.00
47_K	109_L	0.802	1.00
45_S	52_L	0.788	1.00
107_E	111_G	0.787	1.00
54_V	69_T	0.781	1.00
16_Q	20_Q	0.781	1.00
19_F	23_Q	0.780	1.00
112_R	116_M	0.779	1.00
34_G	78_K	0.778	1.00
43_L	105_F	0.777	1.00
42_V	61_M	0.775	1.00
45_S	61_M	0.774	1.00
50_G	96_S	0.769	1.00
29_S	32_K	0.767	1.00
87_T	94_D	0.763	1.00
41_F	61_M	0.761	1.00
114_A	118_R	0.758	1.00
49_H	56_E	0.757	1.00
46_L	81_I	0.754	1.00
73_D	83_R	0.748	1.00
70_L	73_D	0.747	1.00
114_A	117_A	0.742	1.00
103_I	106_E	0.740	1.00
40_L	112_R	0.738	1.00
124_T	128_M	0.736	1.00
136_A	140_Q	0.736	1.00
15_L	19_F	0.736	1.00
25_E	115_I	0.735	1.00
11_I	132_A	0.734	1.00
118_R	121_S	0.732	1.00
129_L	133_H	0.730	1.00
130_Q	137_K	0.727	1.00
110_A	113_K	0.725	1.00
126_E	129_L	0.722	1.00
45_S	57_I	0.717	1.00
72_A	76_E	0.715	1.00
58_A	65_P	0.714	1.00
45_S	49_H	0.710	1.00
129_L	132_A	0.710	1.00
38_A	67_A	0.706	1.00
120_L	128_M	0.702	1.00
42_V	57_I	0.699	1.00
113_K	117_A	0.690	1.00
58_A	68_V	0.681	1.00
29_S	115_I	0.678	1.00
20_Q	24_P	0.677	1.00
46_L	52_L	0.670	1.00
76_E	81_I	0.669	1.00
18_L	138_L	0.666	1.00
25_E	28_E	0.666	1.00
97_L	102_D	0.661	1.00
74_R	77_Q	0.657	1.00
74_R	78_K	0.652	1.00
25_E	118_R	0.651	1.00
115_I	118_R	0.651	1.00
39_Q	71_M	0.625	1.00
23_Q	27_L	0.624	1.00
44_A	48_K	0.618	1.00
46_L	97_L	0.612	1.00
123_L	128_M	0.600	1.00
40_L	105_F	0.599	1.00
134_I	138_L	0.599	1.00
107_E	110_A	0.597	1.00
98_T	101_G	0.591	1.00
68_V	72_A	0.591	1.00
133_H	136_A	0.576	1.00
137_K	141_A	0.575	1.00
15_L	18_L	0.569	1.00
14_S	17_A	0.566	1.00
134_I	141_A	0.565	1.00
26_M	112_R	0.564	1.00
23_Q	26_M	0.561	1.00
28_E	31_E	0.560	1.00
79_N	82_A	0.551	1.00
124_T	137_K	0.541	1.00
54_V	92_V	0.541	1.00
41_F	45_S	0.540	1.00
43_L	47_K	0.532	1.00
38_A	63_V	0.530	1.00
53_K	86_N	0.530	1.00
15_L	135_T	0.528	1.00
44_A	109_L	0.527	1.00
53_K	94_D	0.526	1.00
106_E	110_A	0.525	1.00
55_S	92_V	0.514	1.00
120_L	124_T	0.513	1.00
109_L	113_K	0.510	1.00
85_H	89_D	0.509	1.00
65_P	69_T	0.508	1.00
75_L	80_L	0.506	1.00
84_T	87_T	0.506	1.00
22_I	25_E	0.503	1.00
26_M	29_S	0.503	1.00
36_T	74_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
1s3jA	2	0.929	99.9	0.246	Contact Map
4rguA	4	0.929	99.9	0.25	Contact Map
3bj6A	2	0.9613	99.9	0.252	Contact Map
3cdhA	4	0.8645	99.9	0.268	Contact Map
2gxgA	2	0.9032	99.9	0.273	Contact Map
4mnuA	2	0.9613	99.9	0.274	Contact Map
2rdpA	2	0.9032	99.9	0.275	Contact Map
3e6mA	2	0.9355	99.9	0.275	Contact Map
3fm5A	4	0.9226	99.9	0.277	Contact Map
3cjnA	2	0.9097	99.9	0.277	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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