YEZE - BACSU - GREMLIN Contacts

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YEZE - Uncharacterized HTH-type transcriptional regulator YezE

UniProt:	Q7WY76	Sequences: MGRNKEFDTALVLHRAIEVFGEYGYEGTSLQDLLSHLGIARQSLYDTYGTKRDLFLSAVKSYLEGKNAAVMERLEAPGSVKEAIRDIFQEGVNALRDPERAKACYIINSAIEQIPHDPELARYFERQSKQLEDAFYHGLLRAKDQGELNGEDTDISALARYLNQSRLSLTFIAKVTADMDRLQDHVDVSLSVLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	194 (177)
Sequences:	44557 (34946)
Seq/√Len:	2626.7

ECOLI - COMR NEMR SLMA ACRR YJDC ENVR UIDR RUTR BDCR BETI FABR YBIH RCDA
BACSU - YEZE YVDT YFIR YXAF FADR LMRA BSCR YHGD YDGC PKSA YTTP YVKB YCNC YOBS YVAF YUXN YDES 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
31_Q	41_R	3.924	1.00
23_Y	32_D	3.868	1.00
18_E	36_H	3.538	1.00
49_G	53_D	2.693	1.00
20_F	28_T	2.232	1.00
136_Y	156_S	2.217	1.00
34_L	44_L	2.192	1.00
50_T	53_D	2.115	1.00
8_D	11_L	2.047	1.00
10_A	61_S	2.025	1.00
83_A	141_R	2.004	1.00
9_T	57_S	1.957	1.00
136_Y	140_L	1.941	1.00
19_V	28_T	1.897	1.00
22_E	36_H	1.881	1.00
79_S	82_E	1.833	1.00
19_V	36_H	1.809	1.00
11_L	15_R	1.800	1.00
40_A	43_S	1.785	1.00
31_Q	35_S	1.780	1.00
15_R	36_H	1.779	1.00
19_V	32_D	1.774	1.00
140_L	144_D	1.757	1.00
19_V	23_Y	1.657	1.00
140_L	155_I	1.641	1.00
17_I	61_S	1.636	1.00
10_A	14_H	1.609	1.00
16_A	20_F	1.592	1.00
13_L	57_S	1.544	1.00
57_S	60_K	1.530	1.00
30_L	41_R	1.522	1.00
150_G	153_T	1.515	1.00
15_R	18_E	1.504	1.00
140_L	143_K	1.501	1.00
30_L	45_Y	1.493	1.00
60_K	123_Y	1.481	1.00
71_M	134_A	1.437	1.00
32_D	35_S	1.433	1.00
32_D	36_H	1.411	1.00
141_R	145_Q	1.402	1.00
161_Y	165_S	1.398	1.00
14_H	61_S	1.387	1.00
18_E	22_E	1.384	1.00
29_S	32_D	1.379	1.00
61_S	65_G	1.370	1.00
17_I	62_Y	1.368	1.00
9_T	47_T	1.365	1.00
24_G	28_T	1.364	1.00
17_I	58_A	1.351	1.00
132_E	160_R	1.333	1.00
48_Y	57_S	1.321	1.00
56_L	60_K	1.301	1.00
7_F	11_L	1.291	1.00
142_A	148_L	1.282	1.00
16_A	54_L	1.273	1.00
143_K	150_G	1.266	1.00
30_L	44_L	1.263	1.00
28_T	33_L	1.260	1.00
20_F	25_Y	1.239	1.00
143_K	153_T	1.238	1.00
142_A	147_E	1.230	1.00
25_Y	55_F	1.226	1.00
53_D	57_S	1.216	1.00
56_L	123_Y	1.213	1.00
43_S	46_D	1.212	1.00
23_Y	27_G	1.192	1.00
24_G	27_G	1.181	1.00
132_E	136_Y	1.158	1.00
69_A	90_E	1.156	1.00
89_Q	183_Q	1.151	1.00
43_S	47_T	1.146	1.00
149_N	153_T	1.141	1.00
154_D	157_A	1.131	1.00
15_R	19_V	1.128	1.00
82_E	86_D	1.124	1.00
42_Q	46_D	1.123	1.00
40_A	46_D	1.117	1.00
83_A	138_G	1.110	1.00
8_D	47_T	1.110	1.00
52_R	56_L	1.101	1.00
52_R	117_D	1.098	1.00
13_L	58_A	1.098	1.00
79_S	147_E	1.091	1.00
85_R	89_Q	1.080	1.00
39_I	43_S	1.076	1.00
81_K	85_R	1.072	1.00
15_R	37_L	1.070	1.00
44_L	54_L	1.068	1.00
89_Q	186_V	1.059	1.00
7_F	10_A	1.057	1.00
5_K	46_D	1.052	1.00
45_Y	50_T	1.051	1.00
123_Y	126_R	1.036	1.00
86_D	89_Q	1.032	1.00
52_R	119_E	1.030	1.00
80_V	145_Q	1.022	1.00
108_N	112_E	1.020	1.00
13_L	48_Y	1.010	1.00
14_H	18_E	1.007	1.00
60_K	64_E	1.006	1.00
136_Y	155_I	1.005	1.00
41_R	45_Y	1.004	1.00
33_L	54_L	1.003	1.00
67_N	130_Q	0.998	1.00
157_A	184_D	0.998	1.00
129_K	133_D	0.996	1.00
164_Q	168_S	0.991	1.00
53_D	56_L	0.980	1.00
82_E	85_R	0.977	1.00
143_K	155_I	0.975	1.00
94_A	98_P	0.970	1.00
181_R	184_D	0.962	1.00
134_A	137_H	0.951	1.00
137_H	141_R	0.944	1.00
23_Y	36_H	0.941	1.00
61_S	64_E	0.941	1.00
73_R	90_E	0.934	1.00
132_E	156_S	0.932	1.00
71_M	75_E	0.931	1.00
143_K	146_G	0.929	1.00
138_G	142_A	0.922	1.00
17_I	21_G	0.916	1.00
156_S	160_R	0.915	1.00
104_C	108_N	0.914	1.00
137_H	140_L	0.914	1.00
133_D	137_H	0.908	1.00
122_R	126_R	0.908	1.00
57_S	61_S	0.898	1.00
34_L	41_R	0.898	1.00
6_E	10_A	0.898	1.00
116_H	119_E	0.898	1.00
64_E	68_A	0.893	1.00
126_R	130_Q	0.888	1.00
80_V	142_A	0.879	1.00
16_A	58_A	0.879	1.00
69_A	72_E	0.871	1.00
90_E	93_N	0.870	1.00
77_P	83_A	0.865	1.00
178_D	181_R	0.864	1.00
153_T	158_L	0.853	1.00
68_A	72_E	0.849	1.00
8_D	39_I	0.842	1.00
136_Y	159_A	0.839	1.00
41_R	46_D	0.836	1.00
62_Y	65_G	0.835	1.00
141_R	144_D	0.824	1.00
180_D	183_Q	0.824	1.00
86_D	90_E	0.824	1.00
138_G	141_R	0.819	1.00
139_L	162_L	0.816	1.00
26_E	112_E	0.810	1.00
73_R	86_D	0.808	1.00
89_Q	93_N	0.803	1.00
143_K	148_L	0.799	1.00
11_L	14_H	0.789	1.00
19_V	22_E	0.788	1.00
173_A	176_T	0.785	1.00
133_D	136_Y	0.776	1.00
25_Y	51_K	0.773	1.00
5_K	8_D	0.772	1.00
11_L	37_L	0.769	1.00
88_F	162_L	0.766	1.00
67_N	71_M	0.764	1.00
20_F	55_F	0.761	1.00
118_P	122_R	0.758	1.00
13_L	61_S	0.751	1.00
104_C	107_I	0.748	1.00
155_I	159_A	0.738	1.00
23_Y	28_T	0.731	1.00
35_S	41_R	0.731	1.00
139_L	143_K	0.728	1.00
60_K	126_R	0.727	1.00
12_V	37_L	0.720	1.00
139_L	155_I	0.712	1.00
5_K	47_T	0.709	1.00
30_L	34_L	0.706	1.00
14_H	17_I	0.706	1.00
180_D	184_D	0.706	1.00
125_E	129_K	0.700	1.00
37_L	40_A	0.699	1.00
130_Q	133_D	0.698	1.00
12_V	44_L	0.698	1.00
93_N	97_D	0.698	1.00
13_L	17_I	0.691	1.00
123_Y	127_Q	0.687	1.00
121_A	125_E	0.686	1.00
79_S	83_A	0.683	1.00
179_M	183_Q	0.680	1.00
25_Y	52_R	0.676	1.00
164_Q	167_L	0.672	1.00
31_Q	45_Y	0.670	1.00
74_L	134_A	0.669	1.00
150_G	154_D	0.665	1.00
108_N	111_I	0.663	1.00
130_Q	134_A	0.660	1.00
76_A	86_D	0.660	1.00
65_G	68_A	0.658	1.00
77_P	86_D	0.657	1.00
67_N	134_A	0.655	1.00
109_S	112_E	0.654	1.00
72_E	90_E	0.651	1.00
8_D	43_S	0.643	1.00
12_V	47_T	0.642	1.00
5_K	9_T	0.635	1.00
157_A	161_Y	0.627	1.00
112_E	116_H	0.627	1.00
116_H	120_L	0.624	1.00
118_P	121_A	0.621	1.00
22_E	32_D	0.620	1.00
78_G	83_A	0.613	1.00
161_Y	164_Q	0.612	1.00
182_L	185_H	0.611	1.00
81_K	147_E	0.610	1.00
72_E	76_A	0.609	1.00
60_K	127_Q	0.608	1.00
78_G	86_D	0.607	1.00
80_V	147_E	0.607	1.00
68_A	71_M	0.603	1.00
17_I	65_G	0.602	1.00
85_R	88_F	0.600	1.00
8_D	40_A	0.598	1.00
140_L	156_S	0.588	1.00
164_Q	172_I	0.582	1.00
143_K	149_N	0.581	1.00
172_I	176_T	0.573	1.00
63_L	127_Q	0.571	1.00
172_I	175_V	0.570	1.00
6_E	9_T	0.569	1.00
93_N	183_Q	0.566	1.00
91_G	95_L	0.565	1.00
103_A	107_I	0.563	1.00
25_Y	28_T	0.561	1.00
129_K	132_E	0.555	1.00
160_R	172_I	0.555	1.00
157_A	160_R	0.553	1.00
73_R	76_A	0.551	1.00
71_M	130_Q	0.548	1.00
44_L	49_G	0.548	1.00
90_E	94_A	0.546	1.00
122_R	125_E	0.545	1.00
78_G	82_E	0.533	1.00
63_L	130_Q	0.533	1.00
34_L	37_L	0.532	1.00
8_D	12_V	0.532	1.00
83_A	142_A	0.530	1.00
16_A	33_L	0.529	1.00
125_E	128_S	0.527	1.00
105_Y	108_N	0.527	1.00
143_K	147_E	0.525	1.00
134_A	138_G	0.525	1.00
107_I	110_A	0.514	1.00
103_A	106_I	0.514	1.00
26_E	115_P	0.513	1.00
37_L	41_R	0.513	1.00
182_L	186_V	0.508	1.00
34_L	39_I	0.508	1.00
19_V	29_S	0.508	1.00
181_R	186_V	0.508	1.00
168_S	171_F	0.507	1.00
154_D	158_L	0.507	1.00
93_N	96_R	0.506	1.00
42_Q	47_T	0.505	1.00
139_L	158_L	0.504	1.00
92_V	183_Q	0.503	1.00
93_N	182_L	0.502	1.00
31_Q	40_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
3rd3A	2	0.9588	100	0.177	Contact Map
3eupA	2	0.9948	100	0.184	Contact Map
2hyjA	2	0.9845	100	0.185	Contact Map
3qbmA	2	0.9948	100	0.19	Contact Map
2i10A	2	0.9433	100	0.191	Contact Map
3bruA	2	0.9794	100	0.192	Contact Map
4udsA	2	0.9433	100	0.192	Contact Map
3knwA	2	0.933	100	0.195	Contact Map
2g7sA	2	0.9742	100	0.205	Contact Map
4kwaA	2	0.9639	100	0.212	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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