YFIR - BACSU - GREMLIN Contacts

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YFIR - Uncharacterized HTH-type transcriptional regulator YfiR

UniProt:	O31560	Sequences: MSPKVTKEHKDKRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYFSSTEEMFRRIIETGLDEGLRKLDKSAEHQSVWASISSYLDELTEGLRDVADTLAPVQFEYLVTAWRNEERRQYLEKRYDLFVERFSRLLQKGIDQGEFQPVQPLATIAKFFLNMNDGIIQNALYFDEEKADVSGLAESAKLYLKTVLQADEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (183)
Sequences:	44877 (35677)
Seq/√Len:	2637.3

ECOLI - ACRR SLMA RUTR COMR ENVR UIDR NEMR YBIH BDCR BETI FABR YJDC RCDA
BACSU - YFIR FADR YHGD YVDT BSCR YVKB YEZE PKSA YDES YDGC LMRA YTTP YOBS YXAF YVAF YCNC YUXN YERO
HALSA - Q9HRF3 Q9HM72
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
36_K	46_R	3.987	1.00
28_K	37_D	3.940	1.00
23_T	41_E	3.530	1.00
54_S	58_E	2.775	1.00
25_F	33_T	2.450	1.00
55_S	58_E	2.356	1.00
39_V	49_V	2.128	1.00
24_V	41_E	2.117	1.00
14_Q	62_R	2.029	1.00
27_R	41_E	1.983	1.00
24_V	37_D	1.977	1.00
139_S	158_A	1.974	1.00
24_V	28_K	1.942	1.00
24_V	33_T	1.938	1.00
139_S	143_Q	1.926	1.00
20_A	41_E	1.924	1.00
13_R	16_E	1.890	1.00
16_E	20_A	1.890	1.00
15_A	66_T	1.842	1.00
20_A	23_T	1.824	1.00
83_S	86_A	1.807	1.00
36_K	40_E	1.803	1.00
87_S	144_K	1.776	1.00
22_K	66_T	1.658	1.00
45_S	48_G	1.644	1.00
143_Q	157_L	1.625	1.00
15_A	19_E	1.565	1.00
18_L	62_R	1.563	1.00
35_M	46_R	1.552	1.00
143_Q	146_I	1.551	1.00
23_T	27_R	1.538	1.00
35_M	50_Y	1.525	1.00
14_Q	52_Y	1.514	1.00
37_D	41_E	1.509	1.00
34_T	37_D	1.505	1.00
143_Q	147_D	1.493	1.00
62_R	65_E	1.492	1.00
22_K	67_G	1.490	1.00
159_T	191_S	1.463	1.00
37_D	40_E	1.463	1.00
21_A	25_F	1.449	1.00
163_F	167_M	1.401	1.00
53_F	62_R	1.381	1.00
33_T	38_V	1.379	1.00
61_R	65_E	1.363	1.00
146_I	153_P	1.352	1.00
145_G	150_E	1.335	1.00
76_D	137_R	1.322	1.00
48_G	51_L	1.318	1.00
61_R	126_Y	1.318	1.00
93_D	189_A	1.307	1.00
66_T	70_E	1.305	1.00
12_K	16_E	1.301	1.00
89_S	193_K	1.298	1.00
22_K	63_I	1.292	1.00
21_A	59_M	1.288	1.00
29_G	32_L	1.280	1.00
29_G	33_T	1.262	1.00
89_S	190_E	1.262	1.00
20_A	24_V	1.261	1.00
35_M	49_V	1.251	1.00
145_G	151_F	1.247	1.00
144_K	148_Q	1.245	1.00
44_F	48_G	1.243	1.00
74_K	94_E	1.234	1.00
65_E	126_Y	1.228	1.00
19_E	66_T	1.207	1.00
28_K	32_L	1.180	1.00
46_R	50_Y	1.155	1.00
112_E	116_T	1.148	1.00
146_I	154_V	1.141	1.00
135_V	162_K	1.135	1.00
86_A	90_S	1.134	1.00
85_W	89_S	1.133	1.00
89_S	93_D	1.131	1.00
49_V	59_M	1.115	1.00
45_S	51_L	1.112	1.00
93_D	186_S	1.112	1.00
57_E	61_R	1.097	1.00
112_E	115_V	1.097	1.00
108_P	112_E	1.094	1.00
47_G	51_L	1.092	1.00
184_D	187_G	1.091	1.00
25_F	30_F	1.078	1.00
156_P	159_T	1.077	1.00
90_S	93_D	1.075	1.00
135_V	139_S	1.072	1.00
93_D	190_E	1.062	1.00
57_E	120_N	1.052	1.00
58_E	62_R	1.050	1.00
20_A	42_S	1.050	1.00
18_L	53_F	1.049	1.00
87_S	141_L	1.048	1.00
137_R	140_R	1.042	1.00
13_R	52_Y	1.035	1.00
30_F	60_F	1.033	1.00
12_K	15_A	1.026	1.00
22_K	26_K	1.024	1.00
58_E	61_R	1.023	1.00
141_L	145_G	1.022	1.00
48_G	52_Y	1.018	1.00
82_Q	90_S	1.013	1.00
81_H	87_S	1.011	1.00
93_D	193_K	1.008	1.00
19_E	23_T	0.996	1.00
57_E	122_E	0.995	1.00
72_L	133_L	0.980	1.00
139_S	157_L	0.977	1.00
18_L	63_I	0.977	1.00
18_L	66_T	0.971	1.00
65_E	69_D	0.971	1.00
10_K	51_L	0.960	1.00
28_K	41_E	0.956	1.00
50_Y	55_S	0.956	1.00
38_V	59_M	0.942	1.00
21_A	63_I	0.933	1.00
146_I	149_G	0.926	1.00
126_Y	129_K	0.926	1.00
39_V	46_R	0.920	1.00
86_A	89_S	0.918	1.00
74_K	77_K	0.913	1.00
107_A	110_Q	0.913	1.00
146_I	157_L	0.913	1.00
78_S	94_E	0.905	1.00
140_R	144_K	0.900	1.00
65_E	130_R	0.897	1.00
190_E	194_L	0.880	1.00
141_L	144_K	0.880	1.00
90_S	94_E	0.878	1.00
94_E	97_E	0.874	1.00
159_T	187_G	0.874	1.00
83_S	150_E	0.871	1.00
13_R	44_F	0.868	1.00
62_R	66_T	0.866	1.00
78_S	90_S	0.866	1.00
107_A	111_F	0.865	1.00
166_N	170_G	0.864	1.00
66_T	69_D	0.858	1.00
40_E	46_R	0.858	1.00
72_L	76_D	0.857	1.00
93_D	97_E	0.853	1.00
140_R	143_Q	0.849	1.00
24_V	27_R	0.848	1.00
46_R	51_L	0.848	1.00
132_D	136_E	0.841	1.00
187_G	191_S	0.836	1.00
191_S	194_L	0.831	1.00
139_S	161_A	0.830	1.00
16_E	42_S	0.823	1.00
135_V	158_A	0.822	1.00
136_E	140_R	0.817	1.00
73_R	77_K	0.813	1.00
189_A	192_A	0.812	1.00
98_G	102_V	0.809	1.00
67_G	70_E	0.808	1.00
186_S	190_E	0.801	1.00
125_Q	129_K	0.800	1.00
158_A	162_K	0.797	1.00
175_A	178_F	0.797	1.00
129_K	133_L	0.795	1.00
16_E	19_E	0.793	1.00
174_N	177_Y	0.787	1.00
30_F	56_T	0.782	1.00
11_D	15_A	0.779	1.00
146_I	151_F	0.778	1.00
126_Y	130_R	0.775	1.00
9_H	12_K	0.774	1.00
72_L	137_R	0.774	1.00
84_V	148_Q	0.771	1.00
189_A	193_K	0.768	1.00
10_K	13_R	0.758	1.00
102_V	105_T	0.754	1.00
108_P	116_T	0.745	1.00
23_T	104_D	0.744	1.00
17_I	49_V	0.743	1.00
28_K	33_T	0.740	1.00
89_S	194_L	0.739	1.00
17_I	42_S	0.738	1.00
124_R	128_E	0.732	1.00
70_E	73_R	0.729	1.00
121_E	125_Q	0.726	1.00
82_Q	86_A	0.722	1.00
173_Q	177_Y	0.721	1.00
166_N	169_D	0.717	1.00
121_E	124_R	0.715	1.00
69_D	73_R	0.714	1.00
191_S	195_Y	0.711	1.00
84_V	145_G	0.706	1.00
144_K	147_D	0.705	1.00
190_E	193_K	0.698	1.00
111_F	115_V	0.694	1.00
133_L	137_R	0.690	1.00
100_R	185_V	0.689	1.00
92_L	164_F	0.686	1.00
27_R	37_D	0.683	1.00
185_V	188_L	0.681	1.00
18_L	22_K	0.680	1.00
136_E	139_S	0.674	1.00
13_R	48_G	0.670	1.00
9_H	13_R	0.668	1.00
159_T	162_K	0.668	1.00
35_M	39_V	0.667	1.00
133_L	136_E	0.665	1.00
36_K	50_Y	0.665	1.00
97_E	189_A	0.665	1.00
31_E	116_T	0.653	1.00
19_E	22_K	0.651	1.00
42_S	45_S	0.650	1.00
73_R	76_D	0.649	1.00
81_H	86_A	0.646	1.00
122_E	125_Q	0.632	1.00
159_T	163_F	0.628	1.00
97_E	186_S	0.628	1.00
131_Y	135_V	0.626	1.00
188_L	192_A	0.624	1.00
77_K	94_E	0.624	1.00
142_L	157_L	0.622	1.00
35_M	56_T	0.621	1.00
81_H	90_S	0.619	1.00
30_F	33_T	0.617	1.00
107_A	112_E	0.614	1.00
111_F	114_L	0.611	1.00
108_P	111_F	0.607	1.00
113_Y	116_T	0.601	1.00
89_S	92_L	0.601	1.00
10_K	52_Y	0.594	1.00
174_N	178_F	0.594	1.00
157_L	161_A	0.592	1.00
151_F	156_P	0.586	1.00
142_L	164_F	0.583	1.00
69_D	130_R	0.579	1.00
83_S	87_S	0.579	1.00
146_I	152_Q	0.578	1.00
74_K	98_G	0.574	1.00
84_V	150_E	0.574	1.00
163_F	166_N	0.569	1.00
97_E	101_D	0.566	1.00
98_G	101_D	0.566	1.00
188_L	191_S	0.564	1.00
106_L	109_V	0.563	1.00
128_E	132_D	0.560	1.00
128_E	131_Y	0.557	1.00
30_F	57_E	0.556	1.00
142_L	146_I	0.552	1.00
167_M	192_A	0.551	1.00
25_F	60_F	0.551	1.00
186_S	189_A	0.549	1.00
97_E	185_V	0.546	1.00
166_N	174_N	0.546	1.00
183_A	187_G	0.546	1.00
185_V	189_A	0.545	1.00
116_T	120_N	0.545	1.00
22_K	70_E	0.543	1.00
65_E	129_K	0.539	1.00
42_S	46_R	0.536	1.00
46_R	49_V	0.535	1.00
130_R	133_L	0.534	1.00
120_N	123_R	0.533	1.00
156_P	160_I	0.532	1.00
14_Q	53_F	0.530	1.00
156_P	191_S	0.530	1.00
17_I	52_Y	0.525	1.00
160_I	163_F	0.523	1.00
182_K	186_S	0.521	1.00
95_L	99_L	0.521	1.00
187_G	190_E	0.514	1.00
192_A	196_L	0.513	1.00
125_Q	128_E	0.511	1.00
68_L	130_R	0.511	1.00
36_K	45_S	0.507	1.00
183_A	186_S	0.507	1.00
24_V	34_T	0.504	1.00
162_K	165_L	0.500	1.00
153_P	156_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
4udsA	2	0.9171	100	0.184	Contact Map
1rktA	2	0.9951	100	0.189	Contact Map
4jykA	2	0.9463	100	0.218	Contact Map
2ibdA	2	0.9317	100	0.22	Contact Map
3on2A	1	0.9415	100	0.223	Contact Map
3nrgA	2	0.9756	100	0.223	Contact Map
2xdnA	2	0.9659	100	0.224	Contact Map
3g1oA	2	0.9317	100	0.227	Contact Map
3kz9A	2	0.9756	100	0.235	Contact Map
3npiA	2	0.9415	100	0.236	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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