YCJR - ECOLI - GREMLIN Contacts

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YCJR - Uncharacterized protein YcjR

UniProt:	P76044	Sequences: MKIGTQNQAFFPENILEKFRYIKEMGFDGFEIDGKLLVNNIEEVKAAIKETGLPVTTACGGYDGWIGDFIEERRLNGLKQIERILEALAEVGGKGIVVPAAWGMFTFRLPPMTSPRSLDGDRKMVSDSLRVLEQVAARTGTVVYLEPLNRYQDHMINTLADARRYIVENDLKHVQIIGDFYHMNIEEDNLAQALHDNRDLLGHVHIADNHRYQPGSGTLDFHALFEQLRADNYQGYVVYEGRIRAEDPAQAYRDSLAWLRTC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13915
Length:	262 (226)
Sequences:	16538 (11629)
Seq/√Len:	773.6

ECOLI - YCJR FRLC SGBU ULAE HYI YGBM YIHM
BACSU - IOLI IOLH YFIH IOLE END4
HALSA - END4
SULSO - Q97UI8 Q97UG9 Q97UI3 Q7LX49

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
175_Q	202_G	3.034	1.00
82_E	135_V	2.945	1.00
20_R	51_T	2.796	1.00
45_K	49_K	2.792	1.00
220_D	223_A	2.689	1.00
126_S	168_E	2.567	1.00
86_E	139_T	2.499	1.00
29_G	236_Y	2.459	1.00
208_D	215_G	2.453	1.00
46_A	50_E	2.351	1.00
195_H	227_Q	2.269	1.00
142_V	202_G	2.260	1.00
86_E	135_V	2.245	1.00
14_N	17_E	2.142	1.00
142_V	175_Q	2.096	1.00
144_Y	202_G	2.073	1.00
16_L	47_A	2.010	1.00
134_Q	171_L	1.954	1.00
89_A	139_T	1.914	1.00
164_R	168_E	1.911	1.00
163_R	196_D	1.890	1.00
122_R	164_R	1.872	1.00
78_L	131_V	1.849	1.00
47_A	51_T	1.821	1.00
95_G	144_Y	1.816	1.00
195_H	230_A	1.759	1.00
20_R	24_E	1.752	1.00
75_L	79_K	1.720	1.00
208_D	217_G	1.694	1.00
85_L	139_T	1.686	1.00
48_I	55_V	1.666	1.00
163_R	167_V	1.653	1.00
227_Q	230_A	1.644	1.00
47_A	50_E	1.640	1.00
40_N	43_E	1.637	1.00
133_E	174_V	1.630	1.00
42_E	90_E	1.605	1.00
123_K	168_E	1.601	1.00
189_N	192_Q	1.573	1.00
135_V	138_R	1.565	1.00
122_R	168_E	1.562	1.00
120_G	123_K	1.551	1.00
192_Q	196_D	1.543	1.00
88_L	93_G	1.543	1.00
74_R	128_S	1.507	1.00
222_H	226_E	1.501	1.00
144_Y	177_I	1.492	1.00
38_V	90_E	1.490	1.00
79_K	83_R	1.473	1.00
126_S	130_R	1.463	1.00
23_K	51_T	1.462	1.00
83_R	86_E	1.457	1.00
73_R	76_N	1.449	1.00
134_Q	138_R	1.440	1.00
137_A	173_H	1.433	1.00
117_S	120_G	1.430	1.00
135_V	139_T	1.429	1.00
41_I	90_E	1.423	1.00
123_K	127_D	1.422	1.00
85_L	136_A	1.416	1.00
204_V	228_L	1.412	1.00
158_T	161_D	1.410	1.00
226_E	230_A	1.388	1.00
82_E	131_V	1.386	1.00
180_F	224_L	1.381	1.00
16_L	50_E	1.370	1.00
43_E	46_A	1.354	1.00
137_A	171_L	1.347	1.00
19_F	51_T	1.325	1.00
21_Y	24_E	1.324	1.00
227_Q	231_D	1.324	1.00
191_A	223_A	1.323	1.00
127_D	130_R	1.319	1.00
175_Q	200_L	1.296	1.00
20_R	47_A	1.288	1.00
17_E	20_R	1.282	1.00
46_A	49_K	1.282	1.00
124_M	127_D	1.249	1.00
193_A	197_N	1.242	1.00
79_K	82_E	1.237	1.00
160_A	196_D	1.226	1.00
95_G	142_V	1.217	1.00
130_R	170_D	1.217	1.00
133_E	169_N	1.214	1.00
82_E	86_E	1.204	1.00
43_E	47_A	1.200	1.00
167_V	200_L	1.194	1.00
85_L	141_T	1.193	1.00
140_G	173_H	1.190	1.00
147_P	183_M	1.180	1.00
42_E	46_A	1.169	1.00
16_L	43_E	1.168	1.00
126_S	169_N	1.167	1.00
85_L	135_V	1.158	1.00
78_L	82_E	1.154	1.00
157_N	161_D	1.148	1.00
191_A	195_H	1.148	1.00
45_K	90_E	1.144	1.00
164_R	167_V	1.142	1.00
27_F	239_Y	1.140	1.00
162_A	176_I	1.135	1.00
178_G	183_M	1.130	1.00
163_R	200_L	1.115	1.00
75_L	131_V	1.114	1.00
81_I	132_L	1.112	1.00
23_K	52_G	1.111	1.00
228_L	231_D	1.110	1.00
198_R	231_D	1.098	1.00
131_V	134_Q	1.096	1.00
130_R	169_N	1.085	1.00
137_A	172_K	1.084	1.00
122_R	126_S	1.073	1.00
19_F	47_A	1.072	1.00
70_I	73_R	1.072	1.00
207_A	211_R	1.059	1.00
136_A	143_V	1.056	1.00
21_Y	25_M	1.045	1.00
211_R	214_P	1.041	1.00
163_R	197_N	1.037	1.00
118_L	161_D	1.027	1.00
223_A	227_Q	1.022	1.00
82_E	138_R	1.019	1.00
182_H	207_A	1.010	1.00
29_G	56_T	1.005	1.00
31_E	57_T	0.996	1.00
192_Q	195_H	0.982	1.00
19_F	48_I	0.982	1.00
29_G	54_P	0.980	1.00
86_E	90_E	0.979	1.00
179_D	240_E	0.978	1.00
95_G	202_G	0.973	1.00
71_E	75_L	0.970	1.00
181_Y	207_A	0.968	1.00
38_V	42_E	0.962	1.00
194_L	231_D	0.960	1.00
195_H	231_D	0.958	1.00
119_D	164_R	0.956	1.00
48_I	53_L	0.952	1.00
41_I	45_K	0.949	1.00
16_L	20_R	0.939	1.00
41_I	87_A	0.934	1.00
219_L	224_L	0.932	1.00
94_K	142_V	0.931	1.00
134_Q	137_A	0.930	1.00
31_E	203_H	0.927	1.00
78_L	128_S	0.925	1.00
86_E	89_A	0.918	1.00
76_N	79_K	0.915	1.00
22_I	27_F	0.914	1.00
97_V	177_I	0.908	1.00
213_Q	216_S	0.905	1.00
133_E	171_L	0.905	1.00
54_P	94_K	0.903	1.00
127_D	131_V	0.903	1.00
82_E	139_T	0.902	1.00
181_Y	211_R	0.895	1.00
32_I	55_V	0.894	1.00
184_N	218_T	0.891	1.00
58_A	88_L	0.891	1.00
176_I	197_N	0.889	1.00
23_K	28_D	0.888	1.00
48_I	51_T	0.886	1.00
166_I	200_L	0.882	1.00
119_D	123_K	0.880	1.00
129_L	174_V	0.880	1.00
206_I	221_F	0.879	1.00
191_A	227_Q	0.875	1.00
133_E	173_H	0.875	1.00
88_L	96_I	0.872	1.00
13_E	21_Y	0.871	1.00
169_N	174_V	0.868	1.00
22_I	30_F	0.859	1.00
130_R	134_Q	0.855	1.00
146_E	240_E	0.852	1.00
160_A	164_R	0.851	1.00
74_R	124_M	0.849	1.00
41_I	91_V	0.841	1.00
194_L	227_Q	0.839	1.00
37_L	40_N	0.838	1.00
39_N	43_E	0.827	1.00
207_A	242_R	0.826	1.00
87_A	91_V	0.826	1.00
56_T	236_Y	0.821	1.00
74_R	127_D	0.820	1.00
130_R	171_L	0.806	1.00
122_R	161_D	0.805	1.00
225_F	229_R	0.805	1.00
59_C	99_P	0.803	1.00
42_E	45_K	0.800	1.00
89_A	141_T	0.798	1.00
212_Y	216_S	0.791	1.00
159_L	196_D	0.784	1.00
118_L	121_D	0.780	1.00
45_K	92_G	0.779	1.00
20_R	50_E	0.779	1.00
159_L	188_D	0.779	1.00
28_D	54_P	0.772	1.00
120_G	124_M	0.768	1.00
142_V	173_H	0.768	1.00
130_R	168_E	0.762	1.00
204_V	237_V	0.761	1.00
55_V	93_G	0.759	1.00
156_I	162_A	0.758	1.00
223_A	226_E	0.756	1.00
221_F	225_F	0.750	1.00
180_F	221_F	0.747	1.00
89_A	140_G	0.740	1.00
124_M	128_S	0.740	1.00
184_N	219_L	0.736	1.00
72_E	76_N	0.736	1.00
54_P	236_Y	0.735	1.00
66_I	128_S	0.733	1.00
125_V	165_Y	0.731	1.00
132_L	143_V	0.730	1.00
194_L	197_N	0.727	1.00
203_H	238_V	0.726	1.00
68_D	73_R	0.717	1.00
166_I	176_I	0.710	1.00
59_C	62_Y	0.708	1.00
19_F	30_F	0.707	1.00
177_I	203_H	0.701	1.00
84_I	96_I	0.692	1.00
16_L	51_T	0.691	1.00
80_Q	83_R	0.690	1.00
131_V	135_V	0.689	1.00
83_R	87_A	0.685	1.00
128_S	131_V	0.680	1.00
78_L	132_L	0.678	1.00
225_F	237_V	0.676	1.00
18_K	22_I	0.675	1.00
19_F	23_K	0.672	1.00
232_N	235_G	0.672	1.00
178_G	194_L	0.670	1.00
95_G	203_H	0.667	1.00
156_I	165_Y	0.666	1.00
31_E	238_V	0.666	1.00
198_R	201_L	0.665	1.00
170_D	200_L	0.660	1.00
198_R	227_Q	0.656	1.00
85_L	96_I	0.655	1.00
206_I	237_V	0.653	1.00
170_D	173_H	0.653	1.00
23_K	53_L	0.651	1.00
74_R	78_L	0.651	1.00
129_L	165_Y	0.646	1.00
161_D	164_R	0.643	1.00
94_K	140_G	0.642	1.00
166_I	170_D	0.642	1.00
147_P	162_A	0.642	1.00
96_I	136_A	0.641	1.00
133_E	143_V	0.638	1.00
13_E	17_E	0.638	1.00
146_E	205_H	0.634	1.00
194_L	201_L	0.633	1.00
166_I	174_V	0.632	1.00
71_E	74_R	0.631	1.00
17_E	21_Y	0.631	1.00
147_P	156_I	0.630	1.00
71_E	124_M	0.628	1.00
121_D	124_M	0.627	1.00
204_V	233_Y	0.624	1.00
126_S	165_Y	0.619	1.00
144_Y	175_Q	0.616	1.00
58_A	61_G	0.614	1.00
146_E	182_H	0.611	1.00
229_R	232_N	0.610	1.00
98_V	143_V	0.609	1.00
133_E	137_A	0.609	1.00
20_R	23_K	0.607	1.00
180_F	206_I	0.605	1.00
203_H	236_Y	0.603	1.00
193_A	196_D	0.602	1.00
125_V	129_L	0.602	1.00
72_E	75_L	0.602	1.00
122_R	165_Y	0.600	1.00
179_D	207_A	0.598	1.00
58_A	93_G	0.594	1.00
184_N	190_L	0.594	1.00
194_L	198_R	0.592	1.00
228_L	233_Y	0.592	1.00
205_H	238_V	0.591	1.00
37_L	41_I	0.585	1.00
199_D	231_D	0.585	1.00
70_I	74_R	0.584	1.00
19_F	44_V	0.584	1.00
154_H	157_N	0.583	1.00
183_M	193_A	0.581	1.00
229_R	237_V	0.581	1.00
99_P	207_A	0.580	1.00
169_N	172_K	0.580	1.00
210_H	213_Q	0.576	1.00
136_A	141_T	0.575	1.00
74_R	131_V	0.573	1.00
194_L	224_L	0.569	1.00
163_R	166_I	0.568	1.00
178_G	193_A	0.565	1.00
178_G	201_L	0.565	1.00
190_L	193_A	0.561	1.00
134_Q	173_H	0.560	1.00
49_K	90_E	0.560	1.00
159_L	163_R	0.559	1.00
92_G	141_T	0.558	1.00
19_F	53_L	0.558	1.00
88_L	141_T	0.558	1.00
78_L	135_V	0.557	1.00
97_V	203_H	0.556	1.00
61_G	84_I	0.554	1.00
99_P	182_H	0.553	1.00
100_A	103_G	0.550	1.00
77_G	80_Q	0.550	1.00
176_I	201_L	0.547	1.00
165_Y	169_N	0.546	1.00
203_H	233_Y	0.544	1.00
122_R	155_M	0.542	1.00
44_V	47_A	0.541	1.00
60_G	84_I	0.538	1.00
78_L	81_I	0.537	1.00
76_N	80_Q	0.537	1.00
10_F	25_M	0.533	1.00
98_V	129_L	0.531	1.00
129_L	133_E	0.529	1.00
86_E	138_R	0.526	1.00
57_T	97_V	0.523	1.00
38_V	41_I	0.522	1.00
57_T	238_V	0.521	1.00
48_I	52_G	0.521	1.00
207_A	241_G	0.518	1.00
197_N	201_L	0.518	1.00
136_A	139_T	0.514	1.00
159_L	192_Q	0.513	1.00
42_E	49_K	0.512	1.00
241_G	244_R	0.512	1.00
206_I	225_F	0.508	1.00
177_I	182_H	0.505	1.00
10_F	21_Y	0.504	1.00
123_K	126_S	0.502	1.00
162_A	166_I	0.501	1.00
15_I	19_F	0.500	1.00
97_V	182_H	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
1i60A	1	0.9542	100	0.193	Contact Map
3kwsA	2	0.9733	100	0.199	Contact Map
2qulA	2	0.9847	100	0.201	Contact Map
3vniA	4	0.9771	100	0.206	Contact Map
2hk0A	3	0.9733	100	0.206	Contact Map
3vylA	4	0.9695	100	0.209	Contact Map
2zdsA	5	0.9885	100	0.211	Contact Map
3qc0A	2	0.9542	100	0.215	Contact Map
4ovxA	1	0.9389	100	0.219	Contact Map
3cqjA	2	0.9542	100	0.224	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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