YHGD - BACSU - GREMLIN Contacts

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YHGD - Uncharacterized HTH-type transcriptional regulator YhgD

UniProt:	P32398	Sequences: MSIDRKKLILEAATKSFTQFGYKATTMDLVAKLANVGKGTIYTFFKNKEELFDEIFTTLLKEMKQKADEAMEPSLPFHENVHRALFAILEFRKTHQLTIKIFQENAEIGTMAVQEVIQKMERSILSYIKSKIEDGIKSGAIKPCDPELTAFVMLKLYIALIFDWEKQHPPLDKETIAGLLELYVVKGLSAN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	191 (179)
Sequences:	39960 (31452)
Seq/√Len:	2350.8

ECOLI - SLMA RUTR ACRR COMR ENVR UIDR FABR NEMR BETI BDCR YJDC YBIH RCDA
BACSU - YHGD FADR YTTP YVDT YFIR YVKB BSCR LMRA PKSA YXAF YEZE YDGC YVAF YCNC YDES YOBS YUXN YERO YXBF
HALSA - Q9HRF3
SULSO - Q97VV1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_D	38_K	3.907	1.00
20_F	29_L	3.853	1.00
15_K	33_L	3.438	1.00
46_K	50_E	2.684	1.00
17_F	25_T	2.318	1.00
47_N	50_E	2.182	1.00
129_K	147_E	2.104	1.00
31_A	41_I	2.086	1.00
16_S	25_T	2.030	1.00
16_S	29_L	2.013	1.00
16_S	33_L	1.974	1.00
19_Q	33_L	1.926	1.00
129_K	133_E	1.917	1.00
80_N	134_D	1.885	1.00
8_L	12_A	1.880	1.00
12_A	33_L	1.848	1.00
5_R	8_L	1.831	1.00
7_K	58_T	1.830	1.00
6_K	54_E	1.826	1.00
76_P	79_E	1.808	1.00
16_S	20_F	1.803	1.00
133_E	146_P	1.781	1.00
28_D	32_K	1.744	1.00
133_E	137_K	1.723	1.00
12_A	15_K	1.711	1.00
136_I	143_P	1.705	1.00
37_G	40_T	1.689	1.00
133_E	136_I	1.615	1.00
14_T	58_T	1.608	1.00
27_M	42_Y	1.584	1.00
10_L	54_E	1.542	1.00
27_M	38_K	1.512	1.00
7_K	11_E	1.462	1.00
54_E	57_T	1.458	1.00
13_A	17_F	1.442	1.00
14_T	59_L	1.435	1.00
29_L	32_K	1.424	1.00
15_K	19_Q	1.424	1.00
68_D	127_Y	1.411	1.00
152_V	156_L	1.388	1.00
86_F	177_A	1.381	1.00
14_T	55_I	1.375	1.00
29_L	33_L	1.373	1.00
25_T	30_V	1.371	1.00
134_D	138_S	1.370	1.00
58_T	62_E	1.361	1.00
45_F	54_E	1.340	1.00
148_L	179_L	1.336	1.00
57_T	116_V	1.334	1.00
26_T	29_L	1.331	1.00
13_A	51_L	1.328	1.00
53_D	57_T	1.315	1.00
82_H	178_G	1.309	1.00
135_G	141_I	1.293	1.00
40_T	43_T	1.284	1.00
136_I	144_C	1.278	1.00
135_G	140_A	1.252	1.00
21_G	25_T	1.241	1.00
12_A	16_S	1.235	1.00
11_E	58_T	1.229	1.00
20_F	24_A	1.222	1.00
27_M	41_I	1.214	1.00
53_D	116_V	1.201	1.00
125_L	151_F	1.195	1.00
78_H	82_H	1.190	1.00
36_V	40_T	1.176	1.00
80_N	131_K	1.154	1.00
37_G	43_T	1.151	1.00
97_L	100_K	1.146	1.00
66_K	87_A	1.142	1.00
6_K	44_F	1.138	1.00
49_E	53_D	1.135	1.00
21_G	24_A	1.133	1.00
86_F	174_E	1.133	1.00
50_E	54_E	1.133	1.00
86_F	178_G	1.131	1.00
39_G	43_T	1.122	1.00
79_E	83_R	1.115	1.00
82_H	86_F	1.110	1.00
42_Y	47_N	1.100	1.00
145_D	148_L	1.092	1.00
136_I	146_P	1.089	1.00
102_F	105_N	1.087	1.00
76_P	140_A	1.085	1.00
125_L	129_K	1.073	1.00
22_Y	52_F	1.072	1.00
172_D	175_T	1.069	1.00
10_L	45_F	1.066	1.00
38_K	42_Y	1.061	1.00
83_R	86_F	1.045	1.00
64_K	123_S	1.044	1.00
66_K	69_E	1.042	1.00
70_A	87_A	1.040	1.00
82_H	181_E	1.037	1.00
17_F	22_Y	1.037	1.00
127_Y	130_S	1.036	1.00
12_A	34_A	1.027	1.00
75_L	83_R	1.016	1.00
50_E	53_D	1.013	1.00
10_L	55_I	1.013	1.00
131_K	135_G	1.012	1.00
155_K	159_A	1.003	1.00
148_L	175_T	1.003	1.00
11_E	15_K	1.002	1.00
49_E	110_T	1.001	1.00
77_F	138_S	1.001	1.00
30_V	51_L	1.000	1.00
99_I	102_F	0.991	1.00
14_T	18_T	0.989	1.00
116_V	119_K	0.981	1.00
40_T	44_F	0.978	1.00
15_K	97_L	0.963	1.00
20_F	33_L	0.958	1.00
49_E	112_A	0.951	1.00
91_F	95_H	0.946	1.00
57_T	61_K	0.936	1.00
41_I	51_L	0.928	1.00
74_S	80_N	0.926	1.00
130_S	134_D	0.924	1.00
5_R	44_F	0.923	1.00
79_E	82_H	0.922	1.00
144_C	149_T	0.919	1.00
129_K	146_P	0.918	1.00
54_E	58_T	0.917	1.00
70_A	83_R	0.908	1.00
77_F	135_G	0.896	1.00
126_S	130_S	0.894	1.00
59_L	62_E	0.888	1.00
122_R	126_S	0.885	1.00
134_D	137_K	0.884	1.00
119_K	123_S	0.879	1.00
178_G	182_L	0.876	1.00
130_S	133_E	0.875	1.00
109_G	112_A	0.873	1.00
58_T	61_K	0.871	1.00
31_A	38_K	0.868	1.00
86_F	90_E	0.862	1.00
13_A	55_I	0.861	1.00
125_L	147_E	0.861	1.00
38_K	43_T	0.855	1.00
87_A	90_E	0.853	1.00
147_E	151_F	0.840	1.00
82_H	182_L	0.840	1.00
83_R	87_A	0.839	1.00
131_K	134_D	0.834	1.00
175_T	179_L	0.827	1.00
179_L	182_L	0.824	1.00
174_E	178_G	0.820	1.00
16_S	19_Q	0.819	1.00
169_P	172_D	0.809	1.00
100_K	104_E	0.792	1.00
148_L	152_V	0.791	1.00
10_L	58_T	0.790	1.00
115_E	119_K	0.789	1.00
18_T	97_L	0.789	1.00
75_L	79_E	0.787	1.00
9_I	41_I	0.783	1.00
8_L	34_A	0.780	1.00
61_K	65_Q	0.780	1.00
32_K	38_K	0.775	1.00
5_R	36_V	0.774	1.00
85_L	153_M	0.762	1.00
111_M	115_E	0.760	1.00
177_A	181_E	0.759	1.00
64_K	68_D	0.756	1.00
129_K	150_A	0.752	1.00
86_F	181_E	0.752	1.00
126_S	129_K	0.751	1.00
177_A	180_L	0.746	1.00
123_S	127_Y	0.738	1.00
136_I	139_G	0.736	1.00
93_K	173_K	0.734	1.00
164_W	167_Q	0.732	1.00
62_E	65_Q	0.731	1.00
64_K	127_Y	0.729	1.00
65_Q	69_E	0.726	1.00
114_Q	118_Q	0.720	1.00
132_I	146_P	0.713	1.00
116_V	120_M	0.708	1.00
132_I	136_I	0.705	1.00
101_I	105_N	0.704	1.00
97_L	101_I	0.699	1.00
118_Q	122_R	0.699	1.00
90_E	174_E	0.698	1.00
9_I	34_A	0.694	1.00
179_L	183_Y	0.694	1.00
155_K	158_I	0.692	1.00
8_L	11_E	0.692	1.00
57_T	119_K	0.683	1.00
146_P	150_A	0.680	1.00
132_I	153_M	0.680	1.00
20_F	25_T	0.680	1.00
123_S	126_S	0.677	1.00
5_R	37_G	0.677	1.00
11_E	14_T	0.674	1.00
136_I	141_I	0.673	1.00
97_L	105_N	0.671	1.00
90_E	177_A	0.669	1.00
74_S	79_E	0.665	1.00
76_P	80_N	0.665	1.00
17_F	52_F	0.659	1.00
19_Q	29_L	0.656	1.00
22_Y	48_K	0.651	1.00
148_L	151_F	0.651	1.00
77_F	140_A	0.649	1.00
5_R	40_T	0.646	1.00
57_T	120_M	0.644	1.00
118_Q	121_E	0.643	1.00
69_E	87_A	0.642	1.00
174_E	177_A	0.638	1.00
22_Y	49_E	0.635	1.00
82_H	85_L	0.630	1.00
152_V	155_K	0.623	1.00
111_M	114_Q	0.622	1.00
10_L	14_T	0.619	1.00
136_I	142_K	0.618	1.00
34_A	37_G	0.617	1.00
95_H	98_T	0.616	1.00
27_M	31_A	0.615	1.00
90_E	94_T	0.612	1.00
28_D	42_Y	0.611	1.00
90_E	173_K	0.610	1.00
99_I	103_Q	0.609	1.00
74_S	83_R	0.609	1.00
163_D	167_Q	0.606	1.00
156_L	180_L	0.599	1.00
98_T	101_I	0.594	1.00
171_L	175_T	0.593	1.00
36_V	44_F	0.584	1.00
100_K	105_N	0.583	1.00
88_I	92_R	0.580	1.00
176_I	180_L	0.576	1.00
100_K	103_Q	0.569	1.00
23_K	108_I	0.568	1.00
73_P	83_R	0.565	1.00
143_P	149_T	0.561	1.00
132_I	149_T	0.560	1.00
31_A	36_V	0.560	1.00
173_K	176_I	0.557	1.00
9_I	44_F	0.555	1.00
71_M	127_Y	0.555	1.00
65_Q	68_D	0.548	1.00
61_K	120_M	0.548	1.00
173_K	177_A	0.545	1.00
78_H	140_A	0.544	1.00
171_L	174_E	0.544	1.00
60_L	120_M	0.541	1.00
176_I	179_L	0.537	1.00
145_D	179_L	0.537	1.00
85_L	88_I	0.537	1.00
23_K	105_N	0.536	1.00
38_K	41_I	0.534	1.00
175_T	178_G	0.533	1.00
163_D	166_K	0.532	1.00
16_S	26_T	0.525	1.00
62_E	66_K	0.514	1.00
98_T	104_E	0.514	1.00
5_R	43_T	0.512	1.00
27_M	48_K	0.512	1.00
22_Y	25_T	0.511	1.00
87_A	91_F	0.511	1.00
80_N	135_G	0.511	1.00
121_E	125_L	0.510	1.00
178_G	181_E	0.509	1.00
119_K	122_R	0.504	1.00
155_K	163_D	0.502	1.00
104_E	108_I	0.501	1.00
53_D	115_E	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
2ibdA	2	0.9948	100	0.216	Contact Map
4udsA	2	0.9634	100	0.22	Contact Map
1vi0A	2	0.9843	100	0.224	Contact Map
3himA	2	0.9948	100	0.226	Contact Map
4jykA	2	0.9948	100	0.229	Contact Map
3ppbA	2	0.9843	100	0.229	Contact Map
3dcfA	2	0.9581	100	0.23	Contact Map
2genA	2	0.9791	100	0.23	Contact Map
3npiA	2	0.9948	100	0.23	Contact Map
3dewA	2	0.9738	100	0.231	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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