YOBB - ECOLI - GREMLIN Contacts

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YOBB - Uncharacterized protein YobB

UniProt:	P76280	Sequences: MSFWKVAAAQYEPRKTSLTEQVAHHLEFVRAAARQQCQLLVFPSLSLLGCDYSRRALPAPPDLSLLDPLCYAATTWRMTIIAGLPVEYNDRFIRGIAVFAPWRKTPGIYHQSHGACLGRRSRTITVVDEQPQGMDMDPTCSLFTTGQCLGEPDLLASARRLQFFSHQYSIAVLMANARGNSALWDEYGRLIVRADRGSLLLVGQRSSQGWQGDIIPLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14030
Length:	218 (209)
Sequences:	13347 (9616)
Seq/√Len:	665.2

ECOLI - YOBB YAFV YBEM
BACSU - MTNU
HALSA - Q9HQZ3
SULSO - Q97ZZ7 Q97WN8 Q981B6

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_K	204_Q	3.045	1.00
118_G	123_T	2.924	1.00
17_S	20_E	2.545	1.00
25_H	46_S	2.432	1.00
84_L	97_A	2.405	1.00
183_L	203_G	2.311	1.00
164_F	167_Q	2.304	1.00
24_H	198_S	2.266	1.00
185_D	189_R	2.241	1.00
7_A	202_V	2.165	1.00
26_L	72_A	2.047	1.00
7_A	37_C	2.034	1.00
158_A	193_R	2.022	1.00
26_L	68_P	2.022	1.00
30_R	76_W	1.966	1.00
8_A	175_A	1.950	1.00
127_V	132_Q	1.911	1.00
8_A	173_L	1.905	1.00
41_V	144_T	1.886	1.00
91_R	110_H	1.885	1.00
141_S	211_Q	1.879	1.00
35_Q	202_V	1.870	1.00
30_R	75_T	1.837	1.00
38_Q	120_R	1.828	1.00
79_T	101_P	1.813	1.00
70_C	99_F	1.812	1.00
194_A	201_L	1.788	1.00
6_V	173_L	1.780	1.00
40_L	78_M	1.759	1.00
24_H	27_E	1.736	1.00
79_T	98_V	1.725	1.00
143_F	170_I	1.710	1.00
26_L	30_R	1.709	1.00
194_A	199_L	1.680	1.00
159_R	162_Q	1.678	1.00
14_R	20_E	1.604	1.00
73_A	80_I	1.592	1.00
96_I	126_V	1.583	1.00
171_A	186_E	1.580	1.00
30_R	72_A	1.576	1.00
86_V	95_G	1.574	1.00
69_L	82_A	1.566	1.00
81_I	98_V	1.557	1.00
161_L	174_M	1.542	1.00
104_K	107_G	1.542	1.00
192_V	201_L	1.535	1.00
184_W	190_L	1.530	1.00
123_T	141_S	1.500	1.00
41_V	175_A	1.483	1.00
81_I	96_I	1.479	1.00
71_Y	75_T	1.478	1.00
37_C	202_V	1.467	1.00
25_H	42_F	1.462	1.00
29_V	80_I	1.458	1.00
9_A	40_L	1.455	1.00
28_F	31_A	1.451	1.00
31_A	35_Q	1.444	1.00
66_L	97_A	1.430	1.00
125_T	135_D	1.419	1.00
81_I	144_T	1.409	1.00
119_R	122_R	1.402	1.00
173_L	183_L	1.391	1.00
39_L	144_T	1.391	1.00
27_E	31_A	1.383	1.00
29_V	40_L	1.378	1.00
209_G	212_G	1.373	1.00
171_A	191_I	1.359	1.00
22_V	68_P	1.336	1.00
124_I	142_L	1.333	1.00
132_Q	143_F	1.320	1.00
79_T	119_R	1.304	1.00
23_A	27_E	1.301	1.00
59_A	63_L	1.297	1.00
9_A	42_F	1.293	1.00
158_A	162_Q	1.292	1.00
72_A	76_W	1.283	1.00
96_I	146_G	1.278	1.00
185_D	191_I	1.274	1.00
98_V	126_V	1.274	1.00
134_M	138_P	1.248	1.00
130_Q	133_G	1.241	1.00
62_D	66_L	1.241	1.00
127_V	145_T	1.230	1.00
20_E	23_A	1.212	1.00
132_Q	145_T	1.195	1.00
32_A	200_L	1.189	1.00
180_N	193_R	1.181	1.00
23_A	68_P	1.173	1.00
19_T	23_A	1.161	1.00
88_Y	93_I	1.158	1.00
47_L	65_L	1.156	1.00
20_E	24_H	1.149	1.00
9_A	200_L	1.147	1.00
66_L	99_F	1.145	1.00
28_F	200_L	1.137	1.00
79_T	100_A	1.129	1.00
180_N	195_D	1.126	1.00
67_D	70_C	1.121	1.00
29_V	72_A	1.120	1.00
86_V	93_I	1.116	1.00
159_R	166_H	1.114	1.00
185_D	209_G	1.113	1.00
9_A	28_F	1.110	1.00
127_V	131_P	1.107	1.00
165_S	172_V	1.102	1.00
24_H	28_F	1.092	1.00
77_R	101_P	1.092	1.00
29_V	78_M	1.091	1.00
59_A	65_L	1.079	1.00
68_P	71_Y	1.076	1.00
140_C	143_F	1.075	1.00
101_P	120_R	1.072	1.00
67_D	71_Y	1.064	1.00
26_L	75_T	1.060	1.00
81_I	126_V	1.052	1.00
11_Y	28_F	1.037	1.00
142_L	173_L	1.028	1.00
161_L	184_W	1.012	1.00
155_L	162_Q	0.987	1.00
158_A	182_A	0.983	1.00
22_V	26_L	0.975	1.00
72_A	75_T	0.972	1.00
161_L	172_V	0.970	1.00
69_L	80_I	0.970	1.00
154_L	180_N	0.966	1.00
5_K	202_V	0.963	1.00
93_I	110_H	0.961	1.00
161_L	182_A	0.957	1.00
68_P	72_A	0.957	1.00
37_C	40_L	0.949	1.00
133_G	168_Y	0.943	1.00
14_R	17_S	0.938	1.00
5_K	35_Q	0.935	1.00
208_Q	212_G	0.927	1.00
82_A	99_F	0.927	1.00
165_S	184_W	0.925	1.00
98_V	117_L	0.923	1.00
119_R	124_I	0.922	1.00
182_A	190_L	0.922	1.00
136_M	170_I	0.912	1.00
25_H	69_L	0.909	1.00
71_Y	74_T	0.905	1.00
60_P	87_E	0.901	1.00
11_Y	25_H	0.895	1.00
116_C	123_T	0.892	1.00
208_Q	211_Q	0.877	1.00
33_A	78_M	0.877	1.00
26_L	71_Y	0.869	1.00
8_A	201_L	0.866	1.00
19_T	64_S	0.860	1.00
31_A	34_R	0.848	1.00
10_Q	181_S	0.840	1.00
62_D	67_D	0.835	1.00
19_T	68_P	0.834	1.00
190_L	193_R	0.832	1.00
141_S	207_S	0.825	1.00
79_T	120_R	0.825	1.00
38_Q	101_P	0.817	1.00
8_A	183_L	0.816	1.00
155_L	158_A	0.815	1.00
191_I	203_G	0.815	1.00
33_A	76_W	0.813	1.00
30_R	34_R	0.813	1.00
206_S	209_G	0.807	1.00
63_L	67_D	0.806	1.00
116_C	140_C	0.805	1.00
133_G	137_D	0.804	1.00
157_S	174_M	0.803	1.00
63_L	66_L	0.803	1.00
6_V	205_R	0.799	1.00
122_R	125_T	0.795	1.00
18_L	22_V	0.794	1.00
114_G	131_P	0.793	1.00
25_H	82_A	0.786	1.00
11_Y	46_S	0.785	1.00
209_G	213_D	0.781	1.00
45_L	109_Y	0.777	1.00
124_I	144_T	0.773	1.00
12_E	198_S	0.770	1.00
22_V	69_L	0.769	1.00
171_A	205_R	0.761	1.00
29_V	76_W	0.761	1.00
118_G	121_S	0.761	1.00
45_L	50_C	0.759	1.00
35_Q	200_L	0.757	1.00
8_A	181_S	0.755	1.00
159_R	163_F	0.752	1.00
192_V	203_G	0.739	1.00
10_Q	179_G	0.737	1.00
58_P	61_P	0.736	1.00
122_R	142_L	0.733	1.00
73_A	76_W	0.732	1.00
171_A	210_W	0.727	1.00
187_Y	213_D	0.726	1.00
66_L	70_C	0.725	1.00
23_A	26_L	0.724	1.00
45_L	85_P	0.719	1.00
4_W	122_R	0.718	1.00
61_P	66_L	0.715	1.00
207_S	211_Q	0.712	1.00
129_E	133_G	0.706	1.00
7_A	40_L	0.693	1.00
27_E	30_R	0.691	1.00
29_V	42_F	0.689	1.00
7_A	200_L	0.686	1.00
145_T	172_V	0.684	1.00
32_A	40_L	0.681	1.00
48_L	62_D	0.680	1.00
14_R	21_Q	0.678	1.00
17_S	21_Q	0.673	1.00
135_D	140_C	0.673	1.00
18_L	59_A	0.673	1.00
122_R	127_V	0.672	1.00
32_A	37_C	0.670	1.00
122_R	141_S	0.667	1.00
34_R	76_W	0.664	1.00
39_L	79_T	0.660	1.00
41_V	81_I	0.660	1.00
148_C	177_A	0.657	1.00
149_L	153_D	0.655	1.00
87_E	92_F	0.646	1.00
38_Q	121_S	0.645	1.00
195_D	199_L	0.645	1.00
143_F	172_V	0.644	1.00
4_W	121_S	0.643	1.00
169_S	213_D	0.641	1.00
122_R	207_S	0.640	1.00
42_F	46_S	0.640	1.00
79_T	121_S	0.637	1.00
14_R	24_H	0.637	1.00
7_A	32_A	0.637	1.00
39_L	81_I	0.630	1.00
65_L	68_P	0.630	1.00
11_Y	24_H	0.629	1.00
134_M	137_D	0.628	1.00
70_C	73_A	0.627	1.00
25_H	29_V	0.626	1.00
182_A	193_R	0.626	1.00
131_P	135_D	0.620	1.00
189_R	209_G	0.620	1.00
171_A	209_G	0.620	1.00
66_L	82_A	0.619	1.00
4_W	205_R	0.616	1.00
105_T	109_Y	0.615	1.00
160_R	163_F	0.612	1.00
103_R	107_G	0.611	1.00
103_R	109_Y	0.611	1.00
22_V	65_L	0.610	1.00
86_V	97_A	0.610	1.00
85_P	109_Y	0.610	1.00
41_V	173_L	0.609	1.00
84_L	95_G	0.608	1.00
48_L	57_L	0.608	1.00
114_G	117_L	0.605	1.00
18_L	65_L	0.603	1.00
114_G	135_D	0.603	1.00
136_M	168_Y	0.600	1.00
117_L	124_I	0.594	1.00
125_T	140_C	0.591	1.00
39_L	121_S	0.590	1.00
162_Q	190_L	0.587	1.00
129_E	167_Q	0.586	1.00
59_A	62_D	0.583	1.00
61_P	97_A	0.580	1.00
54_R	57_L	0.573	1.00
127_V	135_D	0.572	1.00
12_E	24_H	0.570	1.00
151_E	178_R	0.570	1.00
164_F	168_Y	0.568	1.00
114_G	134_M	0.568	1.00
45_L	94_R	0.568	1.00
83_G	94_R	0.566	1.00
4_W	39_L	0.564	1.00
149_L	157_S	0.564	1.00
55_R	87_E	0.562	1.00
31_A	200_L	0.557	1.00
64_S	67_D	0.557	1.00
151_E	154_L	0.556	1.00
19_T	22_V	0.555	1.00
38_Q	77_R	0.555	1.00
28_F	198_S	0.554	1.00
32_A	78_M	0.554	1.00
176_N	181_S	0.551	1.00
155_L	159_R	0.550	1.00
153_D	157_S	0.547	1.00
154_L	178_R	0.547	1.00
61_P	64_S	0.544	1.00
30_R	33_A	0.543	1.00
26_L	76_W	0.540	1.00
88_Y	91_R	0.534	1.00
150_G	153_D	0.532	1.00
37_C	78_M	0.531	1.00
102_W	107_G	0.530	1.00
116_C	125_T	0.524	0.99
22_V	72_A	0.523	0.99
63_L	87_E	0.523	0.99
46_S	82_A	0.522	0.99
47_L	69_L	0.522	0.99
18_L	57_L	0.521	0.99
123_T	127_V	0.520	0.99
132_Q	164_F	0.518	0.99
102_W	109_Y	0.517	0.99
62_D	84_L	0.516	0.99
141_S	210_W	0.516	0.99
162_Q	184_W	0.511	0.99
8_A	192_V	0.508	0.99
183_L	192_V	0.506	0.99
115_A	138_P	0.506	0.99
158_A	180_N	0.505	0.99
153_D	156_A	0.505	0.99
31_A	199_L	0.505	0.99
100_A	120_R	0.503	0.99
48_L	85_P	0.502	0.99
102_W	106_P	0.500	0.99

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
4izuA	2	0.945	100	0.221	Contact Map
2e11A	2	0.9954	100	0.238	Contact Map
2w1vA	2	0.9954	100	0.244	Contact Map
3ivzA	2	0.9725	100	0.244	Contact Map
2vhhA	5	1	100	0.244	Contact Map
3wuyA	2	0.9908	100	0.246	Contact Map
3p8kA	2	1	100	0.246	Contact Map
2dyuA	5	0.9908	100	0.26	Contact Map
3ilvA	2	0.9083	100	0.273	Contact Map
1f89A	2	1	100	0.274	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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