YCGE - BACSU - GREMLIN Contacts

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YCGE - Uncharacterized HTH-type transcriptional regulator YcgE

UniProt:	O31472	Sequences: MSTRNSRSELEKTAVQLFRKLGTRTVLFHQAAAQALGLFPTDLKSADILNEAGPMTAGELGKKTGLSTGSVTALVDRLEKAGYVAREKDPNDRRRVVIVPLTASKKHIKDLFRPLSESTMDLCREYTEEELELIFSFVGKAADIMEEELERLKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	154 (134)
Sequences:	23682 (17624)
Seq/√Len:	1522.5

ECOLI - MARR SLYA MPRA
BACSU - YCGE YUSO YKOM YFIV YSMB YYBA OHRR YWAE MHQR YETL YXAD YWHA YDCH YDGJ YPOP YDGG YWOH 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
87_E	99_V	3.157	1.00
54_P	99_V	3.131	1.00
130_E	140_K	2.881	1.00
56_T	95_R	2.725	1.00
89_D	97_V	2.605	1.00
85_A	99_V	2.565	1.00
127_T	130_E	2.322	1.00
133_L	137_F	2.169	1.00
133_L	136_S	2.142	1.00
88_K	96_V	2.087	1.00
50_N	108_I	2.053	1.00
42_D	81_A	2.009	1.00
54_P	97_V	1.930	1.00
56_T	59_E	1.921	1.00
130_E	133_L	1.881	1.00
126_Y	137_F	1.828	1.00
125_E	144_I	1.816	1.00
89_D	95_R	1.805	1.00
50_N	100_P	1.742	1.00
103_A	107_H	1.634	1.00
42_D	77_R	1.623	1.00
79_E	86_R	1.595	1.00
134_I	137_F	1.574	1.00
54_P	87_E	1.552	1.00
82_G	103_A	1.541	1.00
57_A	75_V	1.537	1.00
130_E	136_S	1.518	1.00
17_L	139_G	1.513	1.00
45_S	74_L	1.510	1.00
52_A	63_K	1.506	1.00
39_F	42_D	1.506	1.00
75_V	98_I	1.487	1.00
107_H	110_D	1.455	1.00
76_D	80_K	1.397	1.00
48_I	63_K	1.395	1.00
103_A	106_K	1.357	1.00
137_F	140_K	1.339	1.00
50_N	105_K	1.331	1.00
17_L	142_A	1.322	1.00
17_L	135_F	1.290	1.00
67_S	70_S	1.244	1.00
59_E	62_K	1.214	1.00
57_A	96_V	1.209	1.00
36_L	114_P	1.204	1.00
58_G	68_T	1.199	1.00
32_A	114_P	1.190	1.00
76_D	93_R	1.184	1.00
45_S	71_V	1.177	1.00
136_S	140_K	1.176	1.00
58_G	62_K	1.163	1.00
36_L	110_D	1.159	1.00
66_L	70_S	1.155	1.00
86_R	96_V	1.134	1.00
21_L	142_A	1.133	1.00
135_F	139_G	1.092	1.00
69_G	72_T	1.091	1.00
57_A	68_T	1.081	1.00
57_A	71_V	1.076	1.00
131_L	135_F	1.074	1.00
20_K	142_A	1.069	1.00
130_E	137_F	1.068	1.00
30_Q	34_Q	1.066	1.00
106_K	110_D	1.064	1.00
35_A	114_P	1.063	1.00
57_A	98_I	1.056	1.00
55_M	59_E	1.022	1.00
129_E	133_L	1.009	1.00
83_Y	107_H	0.994	1.00
52_A	55_M	0.984	1.00
85_A	101_L	0.972	1.00
76_D	79_E	0.965	1.00
72_T	76_D	0.962	1.00
114_P	117_E	0.948	1.00
87_E	97_V	0.946	1.00
41_T	74_L	0.934	1.00
59_E	63_K	0.930	1.00
81_A	107_H	0.921	1.00
100_P	104_S	0.921	1.00
81_A	103_A	0.916	1.00
66_L	71_V	0.908	1.00
83_Y	103_A	0.908	1.00
55_M	63_K	0.904	1.00
70_S	73_A	0.901	1.00
105_K	109_K	0.890	1.00
102_T	105_K	0.879	1.00
21_L	138_V	0.876	1.00
67_S	73_A	0.871	1.00
88_K	93_R	0.868	1.00
19_R	22_G	0.866	1.00
50_N	112_F	0.863	1.00
43_L	111_L	0.859	1.00
32_A	117_E	0.857	1.00
22_G	26_V	0.851	1.00
32_A	121_D	0.849	1.00
110_D	114_P	0.844	1.00
14_A	135_F	0.836	1.00
49_L	84_V	0.832	1.00
102_T	106_K	0.832	1.00
32_A	118_S	0.828	1.00
128_E	132_E	0.827	1.00
44_K	64_T	0.827	1.00
29_H	32_A	0.826	1.00
36_L	111_L	0.820	1.00
73_A	77_R	0.819	1.00
50_N	109_K	0.818	1.00
53_G	105_K	0.809	1.00
119_T	122_L	0.808	1.00
113_R	117_E	0.801	1.00
133_L	140_K	0.795	1.00
48_I	52_A	0.795	1.00
37_G	81_A	0.791	1.00
77_R	80_K	0.791	1.00
75_V	84_V	0.790	1.00
79_E	85_A	0.789	1.00
115_L	119_T	0.784	1.00
92_D	95_R	0.783	1.00
126_Y	141_A	0.780	1.00
19_R	23_T	0.779	1.00
30_Q	40_P	0.778	1.00
24_R	142_A	0.774	1.00
28_F	118_S	0.769	1.00
118_S	121_D	0.768	1.00
90_P	97_V	0.760	1.00
73_A	76_D	0.758	1.00
45_S	60_L	0.755	1.00
46_A	108_I	0.753	1.00
48_I	64_T	0.752	1.00
89_D	92_D	0.744	1.00
117_E	120_M	0.742	1.00
41_T	70_S	0.742	1.00
121_D	124_R	0.736	1.00
61_G	71_V	0.734	1.00
52_A	59_E	0.731	1.00
123_C	131_L	0.728	1.00
61_G	68_T	0.728	1.00
75_V	79_E	0.724	1.00
18_F	22_G	0.720	1.00
139_G	143_D	0.719	1.00
79_E	84_V	0.719	1.00
45_S	64_T	0.713	1.00
43_L	115_L	0.711	1.00
32_A	35_A	0.709	1.00
48_I	55_M	0.705	1.00
132_E	135_F	0.704	1.00
49_L	100_P	0.704	1.00
113_R	116_S	0.702	1.00
57_A	72_T	0.698	1.00
129_E	132_E	0.695	1.00
100_P	105_K	0.694	1.00
23_T	27_L	0.694	1.00
117_E	121_D	0.689	1.00
77_R	81_A	0.688	1.00
127_T	131_L	0.681	1.00
76_D	86_R	0.680	1.00
116_S	120_M	0.668	1.00
53_G	99_V	0.668	1.00
17_L	20_K	0.662	1.00
47_D	51_E	0.657	1.00
132_E	136_S	0.646	1.00
49_L	55_M	0.641	1.00
110_D	113_R	0.640	1.00
42_D	74_L	0.640	1.00
21_L	141_A	0.634	1.00
71_V	75_V	0.631	1.00
137_F	141_A	0.630	1.00
126_Y	131_L	0.619	1.00
140_K	144_I	0.617	1.00
106_K	109_K	0.617	1.00
101_L	104_S	0.597	1.00
13_T	135_F	0.597	1.00
48_I	60_L	0.590	1.00
25_T	28_F	0.587	1.00
44_K	48_I	0.586	1.00
58_G	61_G	0.575	1.00
26_V	29_H	0.571	1.00
86_R	98_I	0.566	1.00
43_L	108_I	0.565	1.00
82_G	85_A	0.552	1.00
115_L	118_S	0.547	1.00
31_A	34_Q	0.547	1.00
28_F	121_D	0.546	1.00
41_T	66_L	0.545	1.00
137_F	144_I	0.544	1.00
47_D	112_F	0.540	1.00
123_C	127_T	0.539	1.00
14_A	17_L	0.537	1.00
68_T	72_T	0.536	1.00
28_F	31_A	0.535	1.00
58_G	95_R	0.532	1.00
125_E	140_K	0.527	1.00
18_F	138_V	0.520	1.00
46_A	50_N	0.518	1.00
127_T	140_K	0.514	1.00
108_I	112_F	0.509	1.00
26_V	30_Q	0.509	1.00
56_T	89_D	0.507	1.00
38_L	111_L	0.506	1.00
18_F	21_L	0.505	1.00
78_L	83_Y	0.503	1.00
112_F	116_S	0.501	1.00
29_H	115_L	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
3cdhA	4	0.8831	99.9	0.261	Contact Map
3cjnA	2	0.9221	99.9	0.271	Contact Map
3deuA	2	0.8506	99.9	0.274	Contact Map
3e6mA	2	0.9481	99.9	0.275	Contact Map
4mnuA	2	0.9416	99.9	0.275	Contact Map
1z91A	2	0.8896	99.9	0.275	Contact Map
1lj9A	2	0.9286	99.9	0.276	Contact Map
3bj6A	2	0.9675	99.9	0.279	Contact Map
4rguA	4	0.9351	99.9	0.279	Contact Map
3zplA	2	1	99.9	0.283	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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