YDCH - BACSU - GREMLIN Contacts

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YDCH - Uncharacterized HTH-type transcriptional regulator YdcH

UniProt:	P96625	Sequences: MEWHSKFSGPNTSPGFLLWQATQSWQRKVGKALAEFDLTHVQFVLLTSCKYMIAHGETVTQKKLASFSQTNIMMVSEVVRTLEKKGFIERSKNPQDKREVLLSLTEIGGEKVTAALPIVEKIDQAFFAAAMKKENFLSGLQELLKHE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (129)
Sequences:	19159 (14106)
Seq/√Len:	1242.0

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_T	103_S	3.122	1.00
91_S	103_S	3.058	1.00
133_K	142_E	2.711	1.00
93_N	101_L	2.687	1.00
60_T	99_E	2.535	1.00
89_E	103_S	2.513	1.00
135_N	139_G	2.420	1.00
135_N	138_S	2.324	1.00
50_K	112_V	2.066	1.00
58_T	101_L	2.019	1.00
92_K	100_V	2.012	1.00
42_Q	85_K	1.969	1.00
60_T	63_K	1.962	1.00
50_K	104_L	1.776	1.00
93_N	99_E	1.744	1.00
130_A	139_G	1.738	1.00
86_G	107_I	1.606	1.00
32_A	118_I	1.606	1.00
111_K	114_A	1.589	1.00
36_F	118_I	1.586	1.00
42_Q	81_T	1.580	1.00
58_T	91_S	1.562	1.00
107_I	111_K	1.557	1.00
107_I	110_E	1.514	1.00
39_T	42_Q	1.492	1.00
136_F	139_G	1.463	1.00
48_S	67_F	1.462	1.00
61_Q	79_V	1.459	1.00
17_L	141_Q	1.429	1.00
79_V	102_L	1.423	1.00
83_E	90_R	1.414	1.00
36_F	114_A	1.410	1.00
80_R	84_K	1.382	1.00
50_K	109_G	1.310	1.00
45_L	78_V	1.300	1.00
133_K	138_S	1.291	1.00
57_E	109_G	1.289	1.00
139_G	142_E	1.286	1.00
62_K	72_I	1.255	1.00
63_K	66_S	1.254	1.00
70_T	74_M	1.254	1.00
61_Q	100_V	1.252	1.00
56_G	67_F	1.218	1.00
110_E	114_A	1.218	1.00
17_L	137_L	1.192	1.00
138_S	142_E	1.173	1.00
80_R	97_K	1.153	1.00
137_L	141_Q	1.146	1.00
133_K	139_G	1.139	1.00
87_F	111_K	1.139	1.00
30_G	34_A	1.130	1.00
20_Q	144_L	1.129	1.00
36_F	115_A	1.121	1.00
61_Q	102_L	1.114	1.00
62_K	66_S	1.073	1.00
32_A	121_K	1.066	1.00
19_W	22_T	1.054	1.00
132_K	135_N	1.046	1.00
21_A	144_L	1.036	1.00
17_L	144_L	1.035	1.00
32_A	125_A	1.035	1.00
35_E	118_I	1.026	1.00
85_K	111_K	1.024	1.00
45_L	75_V	1.022	1.00
76_S	80_R	1.020	1.00
22_T	26_Q	1.020	1.00
123_D	126_F	1.004	1.00
28_K	122_I	1.000	1.00
90_R	100_V	0.999	1.00
71_N	74_M	0.998	1.00
118_I	121_K	0.996	1.00
85_K	107_I	0.995	1.00
21_A	140_L	0.982	1.00
41_V	78_V	0.981	1.00
14_P	137_L	0.971	1.00
74_M	77_E	0.959	1.00
109_G	113_T	0.958	1.00
61_Q	75_V	0.957	1.00
37_D	85_K	0.954	1.00
87_F	107_I	0.930	1.00
92_K	97_K	0.927	1.00
80_R	83_E	0.924	1.00
59_V	67_F	0.916	1.00
104_L	108_G	0.915	1.00
46_L	112_V	0.910	1.00
106_E	109_G	0.909	1.00
18_L	22_T	0.905	1.00
57_E	103_S	0.898	1.00
59_V	63_K	0.892	1.00
24_S	144_L	0.889	1.00
106_E	110_E	0.889	1.00
30_G	40_H	0.877	1.00
73_M	76_S	0.875	1.00
119_V	123_D	0.874	1.00
50_K	113_T	0.871	1.00
117_P	121_K	0.863	1.00
114_A	118_I	0.859	1.00
79_V	88_I	0.859	1.00
77_E	81_T	0.858	1.00
89_E	105_T	0.857	1.00
70_T	75_V	0.853	1.00
121_K	124_Q	0.845	1.00
91_S	101_L	0.843	1.00
130_A	143_L	0.841	1.00
63_K	67_F	0.834	1.00
49_C	88_I	0.830	1.00
44_V	68_S	0.826	1.00
79_V	83_E	0.825	1.00
94_P	101_L	0.816	1.00
77_E	80_R	0.811	1.00
135_N	142_E	0.808	1.00
32_A	122_I	0.805	1.00
104_L	109_G	0.796	1.00
45_L	64_L	0.788	1.00
121_K	125_A	0.777	1.00
117_P	120_E	0.776	1.00
71_N	77_E	0.775	1.00
82_L	87_F	0.774	1.00
61_Q	72_I	0.761	1.00
134_E	138_S	0.757	1.00
18_L	21_A	0.756	1.00
26_Q	30_G	0.751	1.00
19_W	23_Q	0.747	1.00
43_F	115_A	0.745	1.00
41_V	74_M	0.742	1.00
47_T	51_Y	0.742	1.00
50_K	116_L	0.731	1.00
28_K	125_A	0.727	1.00
49_C	104_L	0.722	1.00
23_Q	27_R	0.717	1.00
134_E	137_L	0.717	1.00
96_D	99_E	0.709	1.00
120_E	124_Q	0.698	1.00
48_S	59_V	0.697	1.00
65_A	75_V	0.688	1.00
65_A	72_I	0.688	1.00
43_F	119_V	0.686	1.00
32_A	35_E	0.685	1.00
83_E	89_E	0.682	1.00
56_G	59_V	0.681	1.00
48_S	68_S	0.670	1.00
64_L	102_L	0.669	1.00
125_A	128_A	0.668	1.00
21_A	143_L	0.666	1.00
122_I	125_A	0.666	1.00
49_C	59_V	0.663	1.00
81_T	84_K	0.659	1.00
116_L	120_E	0.658	1.00
110_E	113_T	0.658	1.00
93_N	96_D	0.652	1.00
75_V	79_V	0.648	1.00
17_L	20_Q	0.646	1.00
114_A	117_P	0.636	1.00
29_V	32_A	0.635	1.00
62_K	65_A	0.629	1.00
47_T	112_V	0.628	1.00
28_K	31_K	0.627	1.00
56_G	63_K	0.627	1.00
45_L	68_S	0.627	1.00
130_A	142_E	0.615	1.00
139_G	143_L	0.614	1.00
127_F	131_M	0.611	1.00
113_T	116_L	0.611	1.00
43_F	112_V	0.609	1.00
38_L	111_K	0.607	1.00
48_S	64_L	0.601	1.00
61_Q	76_S	0.600	1.00
91_S	94_P	0.596	1.00
80_R	90_R	0.596	1.00
44_V	48_S	0.594	1.00
131_M	142_E	0.593	1.00
18_L	25_W	0.593	1.00
20_Q	24_S	0.586	1.00
86_G	89_E	0.585	1.00
47_T	116_L	0.584	1.00
24_S	28_K	0.575	1.00
27_R	31_K	0.570	1.00
113_T	117_P	0.569	1.00
49_C	102_L	0.560	1.00
42_Q	78_V	0.557	1.00
17_L	140_L	0.554	1.00
33_L	43_F	0.548	1.00
61_Q	99_E	0.538	1.00
29_V	119_V	0.535	1.00
83_E	88_I	0.533	1.00
130_A	133_K	0.531	1.00
40_H	44_V	0.527	1.00
112_V	116_L	0.518	1.00
46_L	50_K	0.516	1.00
62_K	99_E	0.512	1.00
129_A	142_E	0.510	1.00
81_T	85_K	0.505	1.00
18_L	140_L	0.500	1.00
31_K	34_A	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
2fbkA	2	0.898	99.9	0.296	Contact Map
3broA	2	0.9388	99.9	0.297	Contact Map
3cdhA	4	0.9048	99.9	0.303	Contact Map
3cjnA	2	0.9456	99.9	0.305	Contact Map
3u2rA	4	0.898	99.9	0.307	Contact Map
4yifA	2	0.9184	99.9	0.308	Contact Map
3e6mA	2	0.9728	99.9	0.31	Contact Map
3deuA	2	0.8639	99.9	0.312	Contact Map
3fm5A	4	0.9592	99.9	0.312	Contact Map
4rguA	4	0.9252	99.9	0.313	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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