YXAF - BACSU - GREMLIN Contacts

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YXAF - Uncharacterized HTH-type transcriptional regulator YxaF

UniProt:	P42105	Sequences: MTSRGDSREKILHTASRLFQLQGYHATGLNQIVKESGAPKGSLYHFFPNGKEELAIEAVTYTGKIVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGLLASETALISEPLRTVCMKVFKSWEAVFARKLMENGFAEEEANQLGTLINSMIEGGIMLSLTNKDKTPLLLIAEQIPVLVRKKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	191 (176)
Sequences:	44296 (34840)
Seq/√Len:	2626.1

ECOLI - NEMR SLMA YJDC COMR RUTR ACRR BETI BDCR ENVR UIDR FABR RCDA YBIH
BACSU - YXAF LMRA FADR YEZE YHGD YTTP PKSA YFIR YVDT YVKB BSCR YCNC YVAF YUXN YDES YDGC YERO YOBS
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
30_N	40_K	4.061	1.00
22_Q	31_Q	3.977	1.00
17_R	35_E	3.560	1.00
48_P	53_E	2.685	1.00
19_F	27_T	2.417	1.00
49_N	53_E	2.159	1.00
33_V	43_L	2.096	1.00
7_S	10_K	2.076	1.00
14_T	35_E	2.058	1.00
9_E	61_Y	2.045	1.00
18_L	35_E	1.997	1.00
10_K	14_T	1.986	1.00
18_L	31_Q	1.971	1.00
21_L	35_E	1.971	1.00
132_E	150_N	1.966	1.00
8_R	57_E	1.903	1.00
18_L	27_T	1.896	1.00
79_D	82_E	1.874	1.00
30_N	34_K	1.788	1.00
18_L	22_Q	1.767	1.00
136_A	140_M	1.754	1.00
132_E	136_A	1.738	1.00
16_S	61_Y	1.730	1.00
39_P	42_S	1.720	1.00
14_T	17_R	1.704	1.00
83_A	137_R	1.679	1.00
9_E	13_H	1.664	1.00
136_A	149_A	1.661	1.00
12_L	57_E	1.657	1.00
15_A	19_F	1.616	1.00
29_L	44_Y	1.568	1.00
29_L	40_K	1.550	1.00
60_T	123_V	1.515	1.00
15_A	54_L	1.498	1.00
61_Y	65_I	1.497	1.00
17_R	21_L	1.484	1.00
31_Q	34_K	1.477	1.00
31_Q	35_E	1.475	1.00
137_R	141_E	1.467	1.00
136_A	139_L	1.458	1.00
57_E	60_T	1.450	1.00
13_H	61_Y	1.438	1.00
139_L	146_E	1.431	1.00
16_S	58_A	1.415	1.00
108_L	112_E	1.414	1.00
155_L	159_M	1.413	1.00
16_S	62_T	1.402	1.00
56_I	60_T	1.401	1.00
89_K	180_A	1.389	1.00
23_G	27_T	1.382	1.00
42_S	45_H	1.382	1.00
47_F	57_E	1.348	1.00
134_V	138_K	1.316	1.00
6_D	10_K	1.308	1.00
28_G	31_Q	1.305	1.00
29_L	43_L	1.277	1.00
27_T	32_I	1.272	1.00
14_T	18_L	1.270	1.00
53_E	57_E	1.251	1.00
6_D	9_E	1.251	1.00
128_F	132_E	1.250	1.00
38_A	42_S	1.219	1.00
23_G	26_A	1.206	1.00
41_G	45_H	1.201	1.00
42_S	46_F	1.200	1.00
24_Y	55_A	1.197	1.00
19_F	24_Y	1.192	1.00
139_L	147_E	1.183	1.00
138_K	144_F	1.179	1.00
69_L	90_K	1.175	1.00
22_Q	26_A	1.171	1.00
85_Q	89_K	1.152	1.00
138_K	143_G	1.148	1.00
104_I	108_L	1.135	1.00
52_E	56_I	1.131	1.00
82_E	86_L	1.121	1.00
12_L	47_F	1.111	1.00
148_E	151_Q	1.109	1.00
40_K	44_Y	1.091	1.00
81_V	85_Q	1.089	1.00
44_Y	49_N	1.085	1.00
14_T	36_S	1.082	1.00
175_P	178_L	1.070	1.00
53_E	56_I	1.066	1.00
43_L	54_L	1.063	1.00
86_L	89_K	1.058	1.00
12_L	58_A	1.055	1.00
56_I	119_P	1.050	1.00
39_P	45_H	1.042	1.00
79_D	143_G	1.041	1.00
49_N	52_E	1.039	1.00
139_L	149_A	1.034	1.00
32_I	54_L	1.032	1.00
8_R	46_F	1.031	1.00
60_T	64_K	1.017	1.00
7_S	46_F	1.001	1.00
151_Q	178_L	1.001	1.00
13_H	17_R	0.994	1.00
139_L	142_N	0.991	1.00
22_Q	35_E	0.977	1.00
158_S	162_G	0.976	1.00
73_S	86_L	0.973	1.00
16_S	20_Q	0.969	1.00
78_S	86_L	0.966	1.00
62_T	65_I	0.964	1.00
89_K	177_L	0.955	1.00
71_Q	130_S	0.950	1.00
7_S	38_A	0.939	1.00
151_Q	182_Q	0.935	1.00
61_Y	64_K	0.931	1.00
82_E	85_Q	0.931	1.00
94_Q	98_T	0.929	1.00
137_R	140_M	0.924	1.00
150_N	154_T	0.921	1.00
69_L	72_Q	0.919	1.00
33_V	40_K	0.915	1.00
73_S	90_K	0.898	1.00
133_A	137_R	0.897	1.00
133_A	136_A	0.896	1.00
85_Q	181_E	0.895	1.00
57_E	61_Y	0.883	1.00
5_G	9_E	0.869	1.00
134_V	137_R	0.867	1.00
128_F	154_T	0.866	1.00
40_K	45_H	0.865	1.00
86_L	90_K	0.864	1.00
90_K	93_S	0.862	1.00
17_R	100_S	0.861	1.00
71_Q	75_D	0.860	1.00
15_A	58_A	0.859	1.00
130_S	133_A	0.859	1.00
129_K	133_A	0.848	1.00
68_H	72_Q	0.847	1.00
77_S	83_A	0.844	1.00
174_T	178_L	0.829	1.00
129_K	132_E	0.822	1.00
64_K	68_H	0.812	1.00
12_L	61_Y	0.799	1.00
10_K	13_H	0.795	1.00
119_P	123_V	0.791	1.00
167_S	170_N	0.788	1.00
139_L	144_F	0.786	1.00
89_K	93_S	0.786	1.00
10_K	36_S	0.784	1.00
78_S	82_E	0.783	1.00
119_P	122_T	0.783	1.00
118_E	122_T	0.780	1.00
67_E	71_Q	0.777	1.00
24_Y	51_K	0.777	1.00
125_M	129_K	0.765	1.00
30_N	44_Y	0.763	1.00
34_K	40_K	0.757	1.00
88_I	156_I	0.756	1.00
149_A	153_G	0.756	1.00
108_L	111_S	0.752	1.00
123_V	126_K	0.750	1.00
113_T	117_S	0.750	1.00
80_P	138_K	0.749	1.00
136_A	150_N	0.740	1.00
112_E	116_I	0.737	1.00
52_E	117_S	0.735	1.00
67_E	130_S	0.735	1.00
77_S	86_L	0.729	1.00
80_P	141_E	0.728	1.00
13_H	16_S	0.727	1.00
18_L	21_L	0.725	1.00
25_H	112_E	0.719	1.00
151_Q	155_L	0.719	1.00
76_E	86_L	0.719	1.00
52_E	119_P	0.719	1.00
151_Q	181_E	0.711	1.00
29_L	33_V	0.706	1.00
126_K	130_S	0.701	1.00
65_I	68_H	0.695	1.00
107_G	111_S	0.695	1.00
179_I	182_Q	0.693	1.00
19_F	55_A	0.691	1.00
11_I	43_L	0.683	1.00
93_S	176_L	0.680	1.00
56_I	123_V	0.676	1.00
22_Q	27_T	0.676	1.00
132_E	153_G	0.674	1.00
132_E	149_A	0.672	1.00
178_L	182_Q	0.672	1.00
92_A	177_L	0.671	1.00
103_G	108_L	0.669	1.00
11_I	36_S	0.668	1.00
21_L	31_Q	0.667	1.00
93_S	97_N	0.667	1.00
107_G	110_A	0.662	1.00
177_L	181_E	0.659	1.00
83_A	138_K	0.653	1.00
11_I	46_F	0.653	1.00
105_P	108_L	0.644	1.00
116_I	120_L	0.643	1.00
103_G	107_G	0.643	1.00
7_S	39_P	0.643	1.00
151_Q	154_T	0.641	1.00
72_Q	90_K	0.639	1.00
135_F	139_L	0.638	1.00
107_G	112_E	0.637	1.00
122_T	126_K	0.636	1.00
118_E	121_R	0.634	1.00
104_I	107_G	0.632	1.00
36_S	39_P	0.631	1.00
176_L	179_I	0.629	1.00
24_Y	52_E	0.629	1.00
114_A	117_S	0.627	1.00
180_A	183_I	0.625	1.00
121_R	124_C	0.625	1.00
178_L	181_E	0.622	1.00
68_H	71_Q	0.621	1.00
85_Q	88_I	0.620	1.00
176_L	180_A	0.617	1.00
155_L	158_S	0.617	1.00
12_L	16_S	0.615	1.00
166_L	170_N	0.612	1.00
148_E	152_L	0.607	1.00
166_L	169_T	0.605	1.00
175_P	180_A	0.604	1.00
80_P	143_G	0.599	1.00
138_K	141_E	0.596	1.00
172_D	175_P	0.592	1.00
91_T	95_F	0.589	1.00
81_V	143_G	0.587	1.00
109_L	113_T	0.585	1.00
16_S	65_I	0.585	1.00
79_D	83_A	0.577	1.00
7_S	42_S	0.575	1.00
33_V	39_P	0.574	1.00
138_K	142_N	0.573	1.00
159_M	162_G	0.572	1.00
83_A	134_V	0.570	1.00
121_R	125_M	0.570	1.00
173_K	177_L	0.559	1.00
72_Q	76_E	0.557	1.00
109_L	112_E	0.552	1.00
90_K	94_Q	0.551	1.00
33_V	38_A	0.550	1.00
161_E	166_L	0.549	1.00
158_S	161_E	0.547	1.00
128_F	150_N	0.545	1.00
174_T	177_L	0.544	1.00
127_V	131_W	0.543	1.00
67_E	126_K	0.541	1.00
36_S	40_K	0.540	1.00
110_A	114_A	0.539	1.00
69_L	94_Q	0.536	1.00
88_I	91_T	0.531	1.00
15_A	32_I	0.530	1.00
117_S	121_R	0.529	1.00
94_Q	97_N	0.527	1.00
33_V	36_S	0.524	1.00
89_K	181_E	0.522	1.00
158_S	166_L	0.521	1.00
154_T	166_L	0.518	1.00
65_I	69_L	0.512	1.00
140_M	149_A	0.511	1.00
73_S	77_S	0.508	1.00
73_S	76_E	0.506	1.00
5_G	8_R	0.505	1.00
113_T	116_I	0.503	1.00
135_F	156_I	0.501	1.00
24_Y	27_T	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
1sgmA	2	0.9581	100	0.208	Contact Map
2g7sA	2	0.9686	100	0.229	Contact Map
2ibdA	2	0.9738	100	0.245	Contact Map
1vi0A	2	0.9634	100	0.246	Contact Map
3qbmA	2	0.9948	100	0.246	Contact Map
3kz9A	2	0.9948	100	0.246	Contact Map
2genA	2	0.9581	100	0.25	Contact Map
3f0cA	2	0.9476	100	0.25	Contact Map
4udsA	2	0.9424	100	0.25	Contact Map
3bruA	2	0.9686	100	0.251	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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