YXAD - BACSU - GREMLIN Contacts

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YXAD - Uncharacterized HTH-type transcriptional regulator YxaD

UniProt:	P42103	Sequences: MQNQNPVELIEYELTTFIRRAVYLDQSEKRTGNLERSSYLLLRQLDEFGPARVKELAESFKLDISTLSRQAAALEAKELIYRFSDPSDGRVSLFTITKLGKQLLKADQQKRLERYEQMLKEWSTQEKEMFGELLQRMNKAFID	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	143 (130)
Sequences:	22489 (16782)
Seq/√Len:	1471.9

ECOLI - SLYA MPRA MARR
BACSU - YXAD YKOM YSMB YFIV YUSO MHQR YYBA YCGE YETL YWAE YWHA OHRR YPOP YDGJ YDGG 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
83_F	95_T	3.162	1.00
50_P	95_T	3.082	1.00
126_E	136_R	2.895	1.00
81_Y	95_T	2.617	1.00
52_R	91_V	2.596	1.00
85_D	93_L	2.498	1.00
123_S	126_E	2.373	1.00
129_M	133_L	2.140	1.00
129_M	132_E	2.130	1.00
46_D	104_L	2.060	1.00
84_S	92_S	2.016	1.00
52_R	55_E	1.953	1.00
38_S	77_K	1.939	1.00
50_P	93_L	1.900	1.00
122_W	133_L	1.853	1.00
126_E	129_M	1.807	1.00
46_D	96_I	1.797	1.00
85_D	91_V	1.727	1.00
99_L	103_L	1.595	1.00
53_V	71_A	1.593	1.00
50_P	83_F	1.588	1.00
38_S	73_A	1.582	1.00
126_E	132_E	1.543	1.00
78_E	99_L	1.542	1.00
75_E	82_R	1.519	1.00
71_A	94_F	1.508	1.00
13_E	135_Q	1.460	1.00
35_E	38_S	1.458	1.00
99_L	102_Q	1.457	1.00
41_L	70_Q	1.453	1.00
133_L	136_R	1.450	1.00
48_F	59_S	1.428	1.00
72_A	76_A	1.422	1.00
130_F	133_L	1.416	1.00
103_L	106_A	1.412	1.00
32_G	110_K	1.374	1.00
46_D	101_K	1.339	1.00
44_Q	59_S	1.305	1.00
55_E	58_E	1.241	1.00
13_E	131_G	1.237	1.00
13_E	138_N	1.228	1.00
54_K	64_I	1.208	1.00
53_V	92_S	1.198	1.00
132_E	136_R	1.193	1.00
63_D	66_T	1.185	1.00
102_Q	106_A	1.176	1.00
54_K	58_E	1.163	1.00
62_L	66_T	1.157	1.00
32_G	106_A	1.134	1.00
72_A	89_G	1.126	1.00
53_V	67_L	1.124	1.00
41_L	67_L	1.103	1.00
17_F	138_N	1.099	1.00
127_K	131_G	1.088	1.00
126_E	133_L	1.083	1.00
79_L	103_L	1.082	1.00
15_T	18_I	1.073	1.00
53_V	64_I	1.071	1.00
53_V	94_F	1.071	1.00
125_Q	129_M	1.067	1.00
51_A	55_E	1.055	1.00
65_S	68_S	1.051	1.00
82_R	92_S	1.022	1.00
26_Q	30_R	1.018	1.00
31_T	110_K	1.017	1.00
28_E	110_K	0.998	1.00
110_K	113_E	0.990	1.00
131_G	135_Q	0.989	1.00
48_F	51_A	0.973	1.00
115_Y	118_M	0.961	1.00
51_A	59_S	0.960	1.00
16_T	138_N	0.953	1.00
66_T	69_R	0.950	1.00
55_E	59_S	0.946	1.00
32_G	107_D	0.943	1.00
77_K	103_L	0.942	1.00
37_S	70_Q	0.925	1.00
98_K	102_Q	0.919	1.00
72_A	75_E	0.916	1.00
96_I	100_G	0.910	1.00
81_Y	97_T	0.910	1.00
98_K	101_K	0.908	1.00
49_G	101_K	0.906	1.00
77_K	99_L	0.905	1.00
79_L	99_L	0.896	1.00
28_E	31_T	0.892	1.00
62_L	67_L	0.891	1.00
68_S	72_A	0.889	1.00
46_D	108_Q	0.885	1.00
83_F	93_L	0.884	1.00
17_F	134_L	0.878	1.00
111_R	115_Y	0.877	1.00
96_I	101_K	0.869	1.00
39_Y	107_D	0.865	1.00
84_S	89_G	0.863	1.00
101_K	105_K	0.862	1.00
63_D	69_R	0.860	1.00
45_L	80_I	0.858	1.00
124_T	128_E	0.851	1.00
46_D	105_K	0.849	1.00
122_W	137_M	0.849	1.00
69_R	73_A	0.847	1.00
113_E	116_E	0.843	1.00
106_A	110_K	0.838	1.00
88_D	91_V	0.837	1.00
69_R	72_A	0.821	1.00
18_I	22_V	0.816	1.00
42_L	104_L	0.809	1.00
109_Q	113_E	0.808	1.00
41_L	56_L	0.796	1.00
71_A	80_I	0.794	1.00
15_T	19_R	0.789	1.00
33_N	77_K	0.787	1.00
20_R	138_N	0.777	1.00
10_I	131_G	0.776	1.00
44_Q	60_F	0.768	1.00
75_E	80_I	0.764	1.00
26_Q	36_R	0.761	1.00
71_A	75_E	0.759	1.00
40_L	60_F	0.759	1.00
73_A	76_A	0.747	1.00
129_M	136_R	0.742	1.00
75_E	81_Y	0.738	1.00
113_E	117_Q	0.731	1.00
44_Q	48_F	0.729	1.00
114_R	117_Q	0.725	1.00
28_E	113_E	0.721	1.00
125_Q	128_E	0.720	1.00
53_V	68_S	0.718	1.00
48_F	55_E	0.718	1.00
14_L	18_I	0.716	1.00
86_P	93_L	0.713	1.00
135_Q	139_K	0.711	1.00
28_E	117_Q	0.709	1.00
39_Y	111_R	0.708	1.00
123_S	127_K	0.707	1.00
19_R	23_Y	0.706	1.00
109_Q	112_L	0.705	1.00
24_L	114_R	0.693	1.00
37_S	66_T	0.691	1.00
22_V	25_D	0.684	1.00
119_L	127_K	0.683	1.00
17_F	137_M	0.681	1.00
102_Q	105_K	0.674	1.00
128_E	132_E	0.673	1.00
49_G	95_T	0.671	1.00
44_Q	51_A	0.671	1.00
57_A	67_L	0.670	1.00
117_Q	120_K	0.668	1.00
128_E	131_G	0.662	1.00
85_D	88_D	0.659	1.00
38_S	70_Q	0.658	1.00
28_E	114_R	0.658	1.00
72_A	82_R	0.647	1.00
41_L	60_F	0.645	1.00
43_R	47_E	0.638	1.00
39_Y	104_L	0.635	1.00
112_L	116_E	0.635	1.00
57_A	64_I	0.632	1.00
22_V	26_Q	0.621	1.00
14_L	17_F	0.610	1.00
73_A	77_K	0.606	1.00
74_L	79_L	0.603	1.00
45_L	96_I	0.601	1.00
13_E	16_T	0.600	1.00
106_A	109_Q	0.599	1.00
44_Q	56_L	0.599	1.00
45_L	51_A	0.596	1.00
67_L	71_A	0.584	1.00
43_R	104_L	0.579	1.00
24_L	117_Q	0.577	1.00
108_Q	112_L	0.570	1.00
122_W	127_K	0.565	1.00
78_E	81_Y	0.563	1.00
16_T	20_R	0.562	1.00
97_T	100_G	0.561	1.00
40_L	44_Q	0.557	1.00
132_E	135_Q	0.550	1.00
105_K	108_Q	0.548	1.00
54_K	91_V	0.545	1.00
52_R	93_L	0.537	1.00
123_S	136_R	0.532	1.00
42_L	46_D	0.529	1.00
37_S	62_L	0.529	1.00
54_K	57_A	0.528	1.00
43_R	108_Q	0.524	1.00
56_L	94_F	0.520	1.00
122_W	136_R	0.520	1.00
24_L	27_S	0.519	1.00
25_D	111_R	0.515	1.00
122_W	126_E	0.514	1.00
21_A	24_L	0.508	1.00
52_R	85_D	0.507	1.00
10_I	130_F	0.504	1.00
83_F	86_P	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
3e6mA	2	1	99.9	0.249	Contact Map
3cjnA	2	0.986	99.9	0.25	Contact Map
3cdhA	4	0.9231	99.9	0.25	Contact Map
2fbkA	2	0.9371	99.9	0.25	Contact Map
3bj6A	2	1	99.9	0.252	Contact Map
4rguA	4	0.979	99.9	0.257	Contact Map
1s3jA	2	1	99.9	0.258	Contact Map
4yifA	2	0.972	99.9	0.259	Contact Map
3deuA	2	0.9091	99.9	0.262	Contact Map
4mnuA	2	0.965	99.9	0.264	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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