YJCO - ECOLI - GREMLIN Contacts

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YJCO - Uncharacterized protein YjcO

UniProt:	P0AF56	Sequences: MKKIIALMLFLTFFAHANDSEPGSQYLKAAEAGDRRAQYFLADSWFSSGDLSKAEYWAQKAADSGDADACALLAQIKITNPVSLDYPQAKVLAEKAAQAGSKEGEVTLAHILVNTQAGKPDYPKAISLLENASEDLENDSAVDAQMLLGLIYANGVGIKADDDKATWYFKRSSAISRTGYSEYWAGMMFLNGEEGFIEKNKQKALHWLNLSCMEGFDTGCEEFEKLTNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11951
Length:	229 (186)
Sequences:	27655 (24461)
Seq/√Len:	1793.6

ECOLI - YJCO YBEQ LPSRP HEMY NLPI YFBP BAMD YGEH PGAA YPHG NRFG BEPA YBET
BACSU - YVCD YPIA RAPB RAPE RAPD RAPJ RAPI RAPG RAPH RAPF YRRB RAPC RAPK RAPA SUNS YSOA GUTR
HALSA - Q9HMM8
SULSO - Q97WM3 Q97V36 Q97VC4 Q97ZS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
161_D	164_K	3.045	1.00
121_D	124_K	2.999	1.00
85_D	88_Q	2.997	1.00
50_D	53_K	2.912	1.00
145_Q	168_Y	2.785	1.00
18_N	21_E	2.683	1.00
105_E	128_L	2.626	1.00
38_Q	57_W	2.616	1.00
70_C	92_L	2.407	1.00
74_A	93_A	2.381	1.00
109_A	129_L	2.338	1.00
42_A	58_A	2.269	1.00
108_L	128_L	2.238	1.00
130_E	148_L	2.199	1.00
149_G	169_F	2.196	1.00
148_L	168_Y	2.132	1.00
41_L	57_W	2.094	1.00
182_E	207_W	2.087	1.00
73_L	92_L	1.990	1.00
59_Q	73_L	1.987	1.00
94_E	108_L	1.970	1.00
126_I	130_E	1.929	1.00
10_F	26_Y	1.909	1.00
27_L	41_L	1.898	1.00
152_Y	168_Y	1.893	1.00
45_W	53_K	1.867	1.00
152_Y	164_K	1.853	1.00
45_W	57_W	1.850	1.00
26_Y	40_F	1.836	1.00
129_L	147_L	1.794	1.00
112_L	128_L	1.746	1.00
13_F	25_Q	1.729	1.00
77_K	92_L	1.721	1.00
58_A	72_L	1.691	1.00
77_K	88_Q	1.678	1.00
112_L	124_K	1.663	1.00
93_A	107_T	1.585	1.00
166_T	170_K	1.547	1.00
186_G	208_L	1.499	1.00
170_K	185_A	1.492	1.00
55_E	59_Q	1.485	1.00
126_I	152_Y	1.485	1.00
13_F	21_E	1.449	1.00
138_N	141_A	1.431	1.00
90_K	94_E	1.421	1.00
126_I	159_K	1.399	1.00
73_L	77_K	1.353	1.00
55_E	77_K	1.322	1.00
145_Q	171_R	1.320	1.00
96_A	104_G	1.302	1.00
148_L	152_Y	1.291	1.00
23_G	45_W	1.282	1.00
23_G	48_S	1.278	1.00
12_T	16_H	1.268	1.00
108_L	112_L	1.251	1.00
205_L	209_N	1.232	1.00
132_A	144_A	1.229	1.00
41_L	45_W	1.219	1.00
23_G	27_L	1.211	1.00
13_F	18_N	1.208	1.00
105_E	131_N	1.205	1.00
169_F	184_W	1.191	1.00
133_S	145_Q	1.187	1.00
152_Y	161_D	1.183	1.00
38_Q	60_K	1.175	1.00
189_F	207_W	1.169	1.00
55_E	83_S	1.169	1.00
45_W	50_D	1.166	1.00
90_K	112_L	1.161	1.00
164_K	167_W	1.148	1.00
70_C	95_K	1.126	1.00
90_K	119_K	1.106	1.00
112_L	121_D	1.097	1.00
183_Y	187_M	1.093	1.00
29_A	37_A	1.088	1.00
113_V	147_L	1.082	1.00
126_I	148_L	1.079	1.00
131_N	135_D	1.055	1.00
61_A	69_A	1.054	1.00
57_W	60_K	1.052	1.00
150_L	184_W	1.043	1.00
173_S	182_E	1.038	1.00
77_K	85_D	1.036	1.00
166_T	189_F	1.032	1.00
39_Y	43_D	1.027	1.00
141_A	144_A	1.023	1.00
43_D	72_L	1.019	1.00
124_K	127_S	1.015	1.00
71_A	75_Q	1.014	1.00
20_S	48_S	1.008	1.00
146_M	150_L	1.003	1.00
62_A	70_C	1.000	1.00
42_A	61_A	0.995	1.00
192_G	195_G	0.988	1.00
75_Q	107_T	0.981	1.00
109_A	125_A	0.973	1.00
195_G	203_K	0.969	1.00
34_D	37_A	0.966	1.00
149_G	172_S	0.965	1.00
185_A	189_F	0.957	1.00
106_V	147_L	0.948	1.00
189_F	203_K	0.945	1.00
53_K	56_Y	0.943	1.00
30_A	38_Q	0.935	1.00
88_Q	91_V	0.932	1.00
66_D	69_A	0.931	1.00
97_A	105_E	0.929	1.00
149_G	165_A	0.929	1.00
146_M	184_W	0.925	1.00
166_T	192_G	0.925	1.00
90_K	108_L	0.912	1.00
171_R	175_I	0.911	1.00
153_A	184_W	0.909	1.00
186_G	204_A	0.909	1.00
55_E	73_L	0.908	1.00
70_C	96_A	0.903	1.00
60_K	64_S	0.903	1.00
122_Y	151_I	0.896	1.00
106_V	144_A	0.890	1.00
52_S	83_S	0.882	1.00
126_I	151_I	0.881	1.00
110_H	147_L	0.880	1.00
106_V	110_H	0.875	1.00
92_L	95_K	0.872	1.00
38_Q	61_A	0.871	1.00
46_F	72_L	0.870	1.00
43_D	47_S	0.870	1.00
11_L	40_F	0.870	1.00
14_F	40_F	0.869	1.00
75_Q	78_I	0.866	1.00
35_R	61_A	0.851	1.00
109_A	132_A	0.847	1.00
23_G	41_L	0.846	1.00
72_L	75_Q	0.845	1.00
184_W	187_M	0.844	1.00
133_S	144_A	0.843	1.00
42_A	54_A	0.843	1.00
39_Y	72_L	0.842	1.00
185_A	207_W	0.841	1.00
101_S	104_G	0.828	1.00
145_Q	172_S	0.827	1.00
178_T	181_S	0.819	1.00
105_E	135_D	0.818	1.00
55_E	76_I	0.817	1.00
123_P	159_K	0.817	1.00
182_E	210_L	0.817	1.00
207_W	210_L	0.807	1.00
128_L	131_N	0.806	1.00
105_E	132_A	0.798	1.00
113_V	154_N	0.795	1.00
21_E	24_S	0.793	1.00
183_Y	186_G	0.791	1.00
78_I	107_T	0.778	1.00
97_A	104_G	0.776	1.00
67_A	96_A	0.775	1.00
153_A	162_D	0.770	1.00
131_N	134_E	0.770	1.00
90_K	111_I	0.768	1.00
76_I	83_S	0.768	1.00
74_A	89_A	0.761	1.00
43_D	46_F	0.761	1.00
147_L	150_L	0.759	1.00
10_F	29_A	0.757	1.00
150_L	153_A	0.754	1.00
87_P	119_K	0.750	1.00
166_T	188_M	0.747	1.00
113_V	122_Y	0.744	1.00
19_D	44_S	0.733	1.00
193_E	201_K	0.732	1.00
171_R	174_A	0.728	1.00
86_Y	111_I	0.726	1.00
142_V	172_S	0.724	1.00
25_Q	28_K	0.723	1.00
11_L	15_A	0.718	1.00
166_T	185_A	0.716	1.00
30_A	41_L	0.715	1.00
168_Y	171_R	0.713	1.00
163_D	192_G	0.712	1.00
23_G	44_S	0.711	1.00
187_M	191_N	0.710	1.00
60_K	63_D	0.709	1.00
164_K	168_Y	0.707	1.00
110_H	113_V	0.706	1.00
38_Q	64_S	0.702	1.00
186_G	211_S	0.702	1.00
132_A	135_D	0.698	1.00
210_L	213_M	0.694	1.00
102_K	132_A	0.693	1.00
122_Y	154_N	0.691	1.00
113_V	151_I	0.690	1.00
39_Y	66_D	0.689	1.00
78_I	86_Y	0.687	1.00
46_F	79_T	0.685	1.00
110_H	114_N	0.683	1.00
151_I	159_K	0.683	1.00
203_K	206_H	0.682	1.00
62_A	69_A	0.682	1.00
124_K	128_L	0.680	1.00
88_Q	92_L	0.675	1.00
113_V	129_L	0.672	1.00
14_F	26_Y	0.670	1.00
210_L	214_E	0.670	1.00
172_S	181_S	0.669	1.00
153_A	169_F	0.669	1.00
74_A	96_A	0.667	1.00
78_I	89_A	0.665	1.00
40_F	43_D	0.663	1.00
153_A	191_N	0.662	1.00
97_A	108_L	0.657	1.00
24_S	28_K	0.657	1.00
78_I	114_N	0.656	1.00
78_I	111_I	0.656	1.00
71_A	104_G	0.652	1.00
39_Y	69_A	0.647	1.00
14_F	44_S	0.644	1.00
95_K	98_Q	0.642	1.00
190_L	208_L	0.641	1.00
122_Y	159_K	0.639	1.00
46_F	76_I	0.638	1.00
106_V	141_A	0.635	1.00
46_F	51_L	0.633	1.00
59_Q	92_L	0.614	1.00
62_A	73_L	0.613	1.00
44_S	48_S	0.612	1.00
51_L	79_T	0.610	1.00
86_Y	114_N	0.608	1.00
113_V	125_A	0.607	1.00
14_F	19_D	0.606	1.00
71_A	107_T	0.603	1.00
167_W	171_R	0.600	1.00
111_I	119_K	0.599	1.00
129_L	151_I	0.599	1.00
107_T	110_H	0.598	1.00
51_L	76_I	0.593	1.00
55_E	85_D	0.591	1.00
30_A	37_A	0.591	1.00
126_I	161_D	0.587	1.00
162_D	191_N	0.587	1.00
150_L	154_N	0.579	1.00
75_Q	79_T	0.578	1.00
145_Q	175_I	0.577	1.00
53_K	57_W	0.572	1.00
166_T	195_G	0.571	1.00
56_Y	60_K	0.571	1.00
128_L	132_A	0.570	1.00
162_D	188_M	0.570	1.00
14_F	47_S	0.568	1.00
172_S	175_I	0.563	1.00
102_K	138_N	0.562	1.00
188_M	192_G	0.556	1.00
106_V	132_A	0.553	1.00
173_S	181_S	0.548	1.00
201_K	205_L	0.547	1.00
61_A	64_S	0.546	1.00
89_A	93_A	0.542	1.00
91_V	95_K	0.542	1.00
153_A	165_A	0.540	1.00
10_F	22_P	0.540	1.00
130_E	168_Y	0.537	1.00
130_E	134_E	0.530	1.00
170_K	174_A	0.528	1.00
167_W	170_K	0.528	1.00
57_W	61_A	0.527	1.00
90_K	121_D	0.522	1.00
127_S	131_N	0.521	1.00
150_L	169_F	0.520	1.00
22_P	44_S	0.519	1.00
19_D	23_G	0.517	1.00
187_M	190_L	0.512	1.00
162_D	166_T	0.511	1.00
22_P	26_Y	0.510	1.00
71_A	101_S	0.510	1.00
94_E	98_Q	0.506	1.00
51_L	55_E	0.506	1.00
110_H	129_L	0.505	1.00
59_Q	77_K	0.505	1.00
206_H	210_L	0.503	1.00
58_A	76_I	0.502	1.00
25_Q	29_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
4ui9C	2	0.917	99.9	0.235	Contact Map
3dssA	1	0.917	99.9	0.236	Contact Map
4rg9A	2	0.8253	99.9	0.241	Contact Map
4ui9J	2	0.917	99.9	0.246	Contact Map
1w3bA	2	0.8996	99.9	0.253	Contact Map
4l9pA	1	0.8996	99.9	0.256	Contact Map
4ui9F	2	0.9083	99.9	0.256	Contact Map
3q7aA	1	0.8821	99.8	0.257	Contact Map
4uzyA	1	0.8646	99.8	0.258	Contact Map
3rjvA	1	0.8952	99.8	0.261	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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