YWAE - BACSU - GREMLIN Contacts

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YWAE - Uncharacterized HTH-type transcriptional regulator YwaE

UniProt:	P25150	Sequences: MERSHQHQQLRKEEHDTLSKLKQMPVESLNLEAISIATNLYRSAQRLRVKMETEVLSTYNLSWTAFSILYDLWVWGALETRKIAELSGISTATASNVIKTLEKKSFCRKSIDTRDRRLVFVSITDSGKQAIEELYPEFHKGETELIAGMTKDEQKILTGLLRKVADNLHTT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	171 (136)
Sequences:	20432 (14864)
Seq/√Len:	1274.6

ECOLI - MPRA SLYA MARR
BACSU - YWAE YETL YFIV YKOM YCGE MHQR YSMB YDGJ YUSO YXAD YYBA YWHA OHRR YDGG YPOP YDCH 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
110_S	122_S	3.207	1.00
153_E	163_K	3.002	1.00
77_A	122_S	2.996	1.00
112_D	120_F	2.920	1.00
79_E	118_L	2.829	1.00
108_R	122_S	2.672	1.00
156_I	160_L	2.587	1.00
150_T	153_E	2.369	1.00
156_I	159_G	2.219	1.00
148_G	167_N	2.194	1.00
73_W	131_I	1.973	1.00
65_A	104_K	1.964	1.00
79_E	82_K	1.957	1.00
77_A	120_F	1.940	1.00
112_D	118_L	1.939	1.00
111_I	119_V	1.911	1.00
153_E	156_I	1.878	1.00
149_M	160_L	1.833	1.00
73_W	123_I	1.782	1.00
126_S	130_A	1.737	1.00
102_E	109_K	1.737	1.00
157_L	160_L	1.670	1.00
130_A	133_E	1.592	1.00
39_N	162_R	1.559	1.00
65_A	100_T	1.548	1.00
59_Y	137_E	1.529	1.00
68_I	97_V	1.523	1.00
71_D	86_L	1.520	1.00
105_S	126_S	1.516	1.00
39_N	158_T	1.506	1.00
62_S	65_A	1.499	1.00
153_E	159_G	1.495	1.00
98_I	121_V	1.481	1.00
126_S	129_Q	1.469	1.00
75_W	86_L	1.460	1.00
77_A	110_S	1.453	1.00
153_E	160_L	1.441	1.00
80_T	98_I	1.428	1.00
39_N	165_A	1.425	1.00
73_W	128_K	1.399	1.00
99_K	103_K	1.398	1.00
160_L	163_K	1.394	1.00
81_R	91_T	1.267	1.00
59_Y	133_E	1.232	1.00
82_K	85_E	1.222	1.00
99_K	116_R	1.220	1.00
129_Q	133_E	1.205	1.00
158_T	162_R	1.202	1.00
109_K	119_V	1.180	1.00
41_Y	44_A	1.174	1.00
68_I	94_A	1.173	1.00
106_F	130_A	1.162	1.00
159_G	163_K	1.160	1.00
42_R	165_A	1.135	1.00
80_T	121_V	1.122	1.00
81_R	85_E	1.115	1.00
80_T	119_V	1.107	1.00
58_T	137_E	1.107	1.00
43_S	165_A	1.105	1.00
90_S	93_T	1.101	1.00
72_L	107_C	1.081	1.00
64_T	97_V	1.067	1.00
89_I	93_T	1.053	1.00
108_R	124_T	1.038	1.00
43_S	161_L	1.036	1.00
92_A	95_S	1.032	1.00
154_Q	158_T	1.018	1.00
152_D	156_I	1.008	1.00
78_L	82_K	1.004	1.00
54_E	137_E	1.000	1.00
106_F	126_S	0.989	1.00
95_S	99_K	0.985	1.00
32_E	155_K	0.962	1.00
98_I	107_C	0.960	1.00
151_K	155_K	0.949	1.00
128_K	132_E	0.947	1.00
80_T	91_T	0.944	1.00
44_A	48_R	0.942	1.00
46_R	165_A	0.939	1.00
110_S	120_F	0.938	1.00
137_E	140_K	0.927	1.00
75_W	78_L	0.924	1.00
59_Y	134_L	0.921	1.00
89_I	94_A	0.919	1.00
104_K	130_A	0.914	1.00
80_T	94_A	0.901	1.00
78_L	86_L	0.898	1.00
82_K	86_L	0.886	1.00
138_F	142_E	0.884	1.00
36_I	158_T	0.884	1.00
73_W	135_Y	0.883	1.00
93_T	96_N	0.878	1.00
52_E	57_S	0.870	1.00
123_I	128_K	0.869	1.00
41_Y	45_Q	0.863	1.00
125_D	128_K	0.863	1.00
156_I	163_K	0.862	1.00
104_K	126_S	0.859	1.00
133_E	137_E	0.838	1.00
136_P	140_K	0.825	1.00
102_E	107_C	0.815	1.00
96_N	100_T	0.814	1.00
141_G	144_E	0.809	1.00
102_E	108_R	0.801	1.00
50_K	141_G	0.795	1.00
68_I	83_I	0.793	1.00
115_D	118_L	0.786	1.00
111_I	116_R	0.779	1.00
67_S	87_S	0.779	1.00
99_K	102_E	0.776	1.00
90_S	96_N	0.773	1.00
125_D	129_Q	0.773	1.00
60_N	104_K	0.769	1.00
76_G	128_K	0.769	1.00
113_T	120_F	0.751	1.00
96_N	99_K	0.739	1.00
54_E	141_G	0.735	1.00
163_K	167_N	0.732	1.00
98_I	102_E	0.729	1.00
140_K	144_E	0.723	1.00
112_D	115_D	0.721	1.00
52_E	63_W	0.720	1.00
84_A	91_T	0.717	1.00
73_W	132_E	0.716	1.00
54_E	144_E	0.714	1.00
152_D	155_K	0.714	1.00
40_L	44_A	0.714	1.00
155_K	159_G	0.708	1.00
100_T	103_K	0.708	1.00
140_K	143_T	0.704	1.00
146_I	154_Q	0.703	1.00
142_E	145_L	0.697	1.00
123_I	127_G	0.696	1.00
136_P	139_H	0.691	1.00
68_I	87_S	0.690	1.00
80_T	95_S	0.688	1.00
39_N	42_R	0.687	1.00
76_G	122_S	0.683	1.00
133_E	136_P	0.678	1.00
71_D	75_W	0.676	1.00
69_L	131_I	0.674	1.00
66_F	134_L	0.667	1.00
40_L	161_L	0.660	1.00
54_E	58_T	0.659	1.00
45_Q	49_V	0.658	1.00
75_W	82_K	0.658	1.00
99_K	109_K	0.657	1.00
64_T	93_T	0.655	1.00
162_R	166_D	0.654	1.00
71_D	87_S	0.651	1.00
94_A	98_I	0.650	1.00
72_L	123_I	0.646	1.00
150_T	154_Q	0.644	1.00
155_K	158_T	0.642	1.00
144_E	147_A	0.635	1.00
149_M	164_V	0.626	1.00
139_H	143_T	0.622	1.00
72_L	78_L	0.622	1.00
71_D	83_I	0.621	1.00
138_F	141_G	0.607	1.00
105_S	108_R	0.605	1.00
100_T	104_K	0.605	1.00
50_K	54_E	0.596	1.00
35_S	158_T	0.596	1.00
66_F	138_F	0.593	1.00
42_R	46_R	0.593	1.00
40_L	43_S	0.592	1.00
109_K	121_V	0.590	1.00
83_I	121_V	0.586	1.00
51_M	138_F	0.580	1.00
43_S	164_V	0.580	1.00
81_R	84_A	0.579	1.00
84_A	94_A	0.577	1.00
101_L	106_F	0.576	1.00
65_A	97_V	0.576	1.00
67_S	71_D	0.568	1.00
50_K	53_T	0.564	1.00
128_K	131_I	0.563	1.00
129_Q	132_E	0.553	1.00
54_E	140_K	0.553	1.00
79_E	120_F	0.545	1.00
70_Y	135_Y	0.543	1.00
39_N	161_L	0.537	1.00
81_R	118_L	0.533	1.00
110_S	113_T	0.530	1.00
71_D	78_L	0.529	1.00
70_Y	74_V	0.529	1.00
32_E	35_S	0.528	1.00
45_Q	48_R	0.528	1.00
148_G	163_K	0.526	1.00
130_A	134_L	0.525	1.00
83_I	94_A	0.522	1.00
43_S	48_R	0.520	1.00
132_E	136_P	0.518	1.00
91_T	95_S	0.518	1.00
135_Y	139_H	0.518	1.00
149_M	154_Q	0.516	1.00
61_L	130_A	0.515	1.00
48_R	52_E	0.512	1.00
84_A	87_S	0.506	1.00
131_I	135_Y	0.503	1.00
50_K	144_E	0.501	1.00
46_R	50_K	0.501	1.00
160_L	167_N	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	0.8713	99.9	0.306	Contact Map
3cjnA	2	0.8421	99.9	0.314	Contact Map
4rguA	4	0.8246	99.9	0.315	Contact Map
3u2rA	4	0.7778	99.9	0.316	Contact Map
3boqA	2	0.8012	99.9	0.321	Contact Map
3e6mA	2	0.883	99.9	0.325	Contact Map
3cdhA	4	0.7895	99.9	0.331	Contact Map
3deuA	2	0.7661	99.9	0.331	Contact Map
3s2wA	3	0.8655	99.9	0.332	Contact Map
2nyxA	2	0.848	99.9	0.333	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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