YKGE - ECOLI - GREMLIN Contacts

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YKGE - Uncharacterized protein YkgE

UniProt:	P77252	Sequences: MNVNFFVTCIGDALKSRMARDSVLLLEKLGCRVNFPEKQGCCGQPAINSGYIKEAIPGMKNLIAALEDNDDPIISPAGSCTYAVKSYPTYLADEPEWASRAAKVAARMQDLTSFIVNKLGVVDVGASLQGRAVYHPSCSLARKLGVKDEPLTLLKNVRGLELLTFAEQDTCCGFGGTFSVKMAEISGEMVKEKVAHLMEVRPEYLIGADVSCLLNISGRLQREGQKVKVMHIAEVLMSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13582
Length:	239 (222)
Sequences:	7322 (4606)
Seq/√Len:	309.1

ECOLI - YKGE GLCF GLPC YDIJ
BACSU - LUTA GLCF FADF
HALSA - Q9HHI4 Q9HNS2 Q9HMZ3 Q9HMR2
SULSO - Q97W77 Q97Z11 Q97VI0 Q97Z15 Q97U61 Q97U89 Q7LX43

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
131_R	161_E	3.624	1.00
24_L	237_M	3.479	1.00
21_D	234_E	3.446	1.00
2_N	32_R	3.427	1.00
131_R	163_L	3.274	1.00
116_V	152_T	3.224	1.00
111_L	233_A	3.118	1.00
51_Y	54_E	2.901	1.00
109_Q	117_N	2.824	1.00
75_S	81_T	2.638	1.00
204_Y	230_M	2.428	1.00
41_C	80_C	2.355	1.00
165_F	197_L	2.274	1.00
22_S	76_P	2.173	1.00
17_R	234_E	2.165	1.00
136_P	151_L	2.140	1.00
22_S	111_L	2.135	1.00
167_E	196_H	2.130	1.00
130_G	204_Y	2.121	1.00
166_A	199_E	2.057	1.00
190_V	219_R	2.043	1.00
2_N	34_N	1.993	1.00
5_F	76_P	1.940	1.00
151_L	164_T	1.936	1.00
2_N	71_D	1.891	1.00
31_C	114_F	1.857	1.00
206_I	235_V	1.828	1.00
4_N	70_D	1.805	1.00
3_V	114_F	1.804	1.00
9_C	41_C	1.802	1.00
151_L	155_K	1.799	1.00
152_T	155_K	1.788	1.00
42_C	80_C	1.769	1.00
47_I	83_A	1.722	1.00
130_G	203_E	1.686	1.00
85_K	113_S	1.678	1.00
11_G	19_A	1.673	1.00
18_M	234_E	1.654	1.00
72_P	107_R	1.647	1.00
133_V	165_F	1.633	1.00
72_P	109_Q	1.619	1.00
56_I	60_K	1.613	1.00
59_M	87_Y	1.609	1.00
195_A	199_E	1.572	1.00
9_C	80_C	1.551	1.00
190_V	215_N	1.531	1.00
117_N	149_E	1.515	1.00
132_A	160_L	1.465	1.00
40_G	61_N	1.459	1.00
131_R	203_E	1.457	1.00
23_V	33_V	1.442	1.00
109_Q	114_F	1.440	1.00
196_H	199_E	1.423	1.00
187_G	219_R	1.400	1.00
60_K	64_A	1.395	1.00
127_S	158_R	1.384	1.00
104_V	108_M	1.378	1.00
132_A	206_I	1.375	1.00
109_Q	113_S	1.373	1.00
154_L	206_I	1.340	1.00
77_A	209_D	1.328	1.00
64_A	67_E	1.301	1.00
28_K	237_M	1.301	1.00
197_L	205_L	1.271	1.00
34_N	70_D	1.270	1.00
132_A	235_V	1.268	1.00
190_V	194_V	1.265	1.00
74_I	114_F	1.265	1.00
113_S	149_E	1.261	1.00
167_E	192_E	1.253	1.00
141_A	147_K	1.243	1.00
61_N	65_A	1.232	1.00
112_T	232_I	1.216	1.00
113_S	117_N	1.214	1.00
167_E	170_T	1.214	1.00
191_K	195_A	1.206	1.00
230_M	234_E	1.201	1.00
133_V	200_V	1.200	1.00
25_L	236_L	1.187	1.00
129_Q	161_E	1.187	1.00
22_S	26_L	1.186	1.00
81_T	144_L	1.182	1.00
183_A	187_G	1.179	1.00
27_E	33_V	1.176	1.00
134_Y	150_P	1.171	1.00
132_A	204_Y	1.161	1.00
81_T	108_M	1.150	1.00
44_Q	79_S	1.149	1.00
146_V	149_E	1.147	1.00
75_S	84_V	1.139	1.00
208_A	232_I	1.135	1.00
155_K	162_L	1.125	1.00
172_C	212_C	1.122	1.00
9_C	42_C	1.120	1.00
73_I	104_V	1.119	1.00
3_V	31_C	1.113	1.00
62_L	84_V	1.112	1.00
4_N	71_D	1.109	1.00
148_D	152_T	1.109	1.00
46_A	54_E	1.103	1.00
8_T	77_A	1.100	1.00
113_S	146_V	1.095	1.00
72_P	114_F	1.091	1.00
20_R	24_L	1.088	1.00
23_V	27_E	1.083	1.00
21_D	237_M	1.083	1.00
7_V	35_F	1.062	1.00
31_C	118_K	1.056	1.00
137_S	207_G	1.050	1.00
59_M	91_L	1.038	1.00
166_A	196_H	1.028	1.00
36_P	39_Q	1.028	1.00
198_M	225_Q	1.016	1.00
205_L	216_I	1.006	1.00
25_L	237_M	0.999	1.00
44_Q	48_N	0.993	1.00
152_T	156_N	0.982	1.00
103_K	107_R	0.981	1.00
114_F	118_K	0.977	1.00
115_I	236_L	0.967	1.00
111_L	115_I	0.955	1.00
197_L	227_V	0.953	1.00
24_L	28_K	0.950	1.00
207_G	213_L	0.950	1.00
120_G	152_T	0.948	1.00
148_D	151_L	0.947	1.00
19_A	23_V	0.942	1.00
103_K	106_A	0.941	1.00
3_V	74_I	0.939	1.00
25_L	233_A	0.938	1.00
133_V	202_P	0.938	1.00
62_L	65_A	0.927	1.00
7_V	39_Q	0.927	1.00
133_V	197_L	0.922	1.00
188_E	191_K	0.921	1.00
55_A	83_A	0.914	1.00
148_D	169_D	0.911	1.00
230_M	235_V	0.905	1.00
183_A	218_G	0.902	1.00
127_S	130_G	0.900	1.00
63_I	67_E	0.898	1.00
195_A	198_M	0.894	1.00
25_L	111_L	0.888	1.00
59_M	90_Y	0.884	1.00
82_Y	143_K	0.883	1.00
168_Q	196_H	0.880	1.00
49_S	177_T	0.869	1.00
5_F	19_A	0.864	1.00
7_V	19_A	0.857	1.00
88_P	105_A	0.854	1.00
154_L	160_L	0.853	1.00
67_E	103_K	0.850	1.00
48_N	79_S	0.844	1.00
133_V	205_L	0.834	1.00
116_V	149_E	0.834	1.00
128_L	160_L	0.831	1.00
131_R	201_R	0.824	1.00
17_R	20_R	0.823	1.00
23_V	35_F	0.815	1.00
129_Q	159_G	0.809	1.00
60_K	94_E	0.802	1.00
47_I	55_A	0.801	1.00
174_F	179_S	0.800	1.00
140_L	146_V	0.799	1.00
65_A	68_D	0.798	1.00
198_M	226_K	0.797	1.00
177_T	181_K	0.796	1.00
53_K	56_I	0.796	1.00
26_L	31_C	0.796	1.00
46_A	58_G	0.795	1.00
109_Q	118_K	0.794	1.00
197_L	216_I	0.793	1.00
86_S	143_K	0.778	0.99
116_V	120_G	0.777	0.99
205_L	227_V	0.776	0.99
54_E	58_G	0.776	0.99
191_K	219_R	0.775	0.99
118_K	121_V	0.774	0.99
57_P	61_N	0.774	0.99
58_G	61_N	0.766	0.99
126_A	130_G	0.765	0.99
75_S	108_M	0.761	0.99
5_F	22_S	0.755	0.99
15_K	210_V	0.750	0.99
165_F	168_Q	0.748	0.99
55_A	59_M	0.748	0.99
58_G	62_L	0.747	0.99
54_E	57_P	0.743	0.99
128_L	204_Y	0.740	0.99
20_R	23_V	0.738	0.99
79_S	139_S	0.737	0.99
187_G	191_K	0.736	0.99
117_N	121_V	0.734	0.99
184_E	188_E	0.733	0.99
127_S	159_G	0.727	0.99
79_S	211_S	0.718	0.99
149_E	152_T	0.716	0.99
18_M	21_D	0.709	0.99
2_N	69_N	0.705	0.99
146_V	150_P	0.704	0.99
57_P	60_K	0.703	0.99
213_L	229_V	0.702	0.99
81_T	85_K	0.700	0.99
194_V	216_I	0.696	0.99
3_V	33_V	0.694	0.99
27_E	32_R	0.694	0.99
16_S	20_R	0.691	0.99
115_I	119_L	0.691	0.99
84_V	104_V	0.687	0.99
206_I	232_I	0.687	0.99
79_S	209_D	0.686	0.99
64_A	68_D	0.686	0.99
91_L	94_E	0.684	0.99
120_G	156_N	0.684	0.99
179_S	186_S	0.677	0.99
140_L	208_A	0.675	0.99
62_L	87_Y	0.674	0.99
66_L	73_I	0.674	0.99
136_P	141_A	0.673	0.99
134_Y	162_L	0.672	0.99
47_I	52_I	0.671	0.98
24_L	27_E	0.669	0.98
122_V	125_G	0.668	0.98
136_P	147_K	0.663	0.98
192_E	195_A	0.660	0.98
22_S	74_I	0.659	0.98
81_T	110_D	0.654	0.98
61_N	64_A	0.654	0.98
26_L	74_I	0.652	0.98
116_V	153_L	0.645	0.98
82_Y	86_S	0.643	0.98
148_D	155_K	0.643	0.98
194_V	198_M	0.643	0.98
174_F	211_S	0.640	0.98
34_N	37_E	0.640	0.98
71_D	107_R	0.638	0.98
4_N	66_L	0.638	0.98
21_D	25_L	0.638	0.98
15_K	18_M	0.637	0.98
77_A	80_C	0.636	0.98
92_A	106_A	0.636	0.98
87_Y	90_Y	0.635	0.98
11_G	18_M	0.634	0.98
15_K	214_L	0.634	0.98
39_Q	66_L	0.627	0.98
8_T	209_D	0.625	0.98
4_N	36_P	0.624	0.98
29_L	118_K	0.624	0.98
26_L	111_L	0.620	0.97
11_G	76_P	0.619	0.97
124_V	156_N	0.619	0.97
89_T	92_A	0.616	0.97
153_L	236_L	0.616	0.97
184_E	187_G	0.616	0.97
134_Y	154_L	0.616	0.97
115_I	153_L	0.610	0.97
130_G	160_L	0.610	0.97
137_S	209_D	0.608	0.97
79_S	174_F	0.608	0.97
162_L	165_F	0.606	0.97
158_R	236_L	0.602	0.97
69_N	72_P	0.601	0.97
205_L	229_V	0.596	0.97
151_L	162_L	0.592	0.97
193_K	196_H	0.590	0.97
21_D	24_L	0.590	0.97
169_D	193_K	0.589	0.97
134_Y	151_L	0.588	0.97
27_E	31_C	0.588	0.97
15_K	213_L	0.588	0.97
112_T	150_P	0.587	0.97
217_S	228_K	0.586	0.96
72_P	75_S	0.585	0.96
107_R	117_N	0.583	0.96
84_V	87_Y	0.580	0.96
85_K	144_L	0.580	0.96
88_P	91_L	0.579	0.96
120_G	123_D	0.579	0.96
151_L	168_Q	0.579	0.96
4_N	34_N	0.578	0.96
45_P	80_C	0.575	0.96
48_N	211_S	0.572	0.96
178_F	189_M	0.570	0.96
22_S	233_A	0.565	0.96
143_K	146_V	0.565	0.96
4_N	7_V	0.564	0.96
25_L	153_L	0.564	0.96
55_A	90_Y	0.564	0.96
78_G	137_S	0.563	0.96
35_F	39_Q	0.562	0.96
112_T	208_A	0.557	0.95
9_C	77_A	0.557	0.95
67_E	105_A	0.556	0.95
78_G	139_S	0.549	0.95
48_N	174_F	0.548	0.95
86_S	89_T	0.548	0.95
4_N	73_I	0.547	0.95
41_C	45_P	0.546	0.95
112_T	116_V	0.544	0.95
142_R	145_G	0.542	0.95
52_I	56_I	0.541	0.95
82_Y	144_L	0.541	0.95
198_M	202_P	0.540	0.94
138_C	171_C	0.540	0.94
178_F	181_K	0.535	0.94
78_G	208_A	0.535	0.94
139_S	215_N	0.533	0.94
139_S	210_V	0.531	0.94
121_V	124_V	0.530	0.94
126_A	129_Q	0.530	0.94
138_C	212_C	0.528	0.94
45_P	48_N	0.528	0.94
63_I	87_Y	0.522	0.93
154_L	162_L	0.519	0.93
6_F	84_V	0.518	0.93
142_R	147_K	0.518	0.93
216_I	229_V	0.518	0.93
118_K	122_V	0.517	0.93
25_L	29_L	0.516	0.93
136_P	150_P	0.514	0.93
118_K	123_D	0.514	0.93
88_P	92_A	0.513	0.93
131_R	228_K	0.511	0.93
44_Q	83_A	0.511	0.93
38_K	68_D	0.510	0.93
119_L	122_V	0.510	0.93
197_L	200_V	0.508	0.93
18_M	213_L	0.508	0.93
163_L	200_V	0.507	0.92
116_V	156_N	0.506	0.92
201_R	227_V	0.502	0.92
178_F	186_S	0.500	0.92
14_L	213_L	0.500	0.92

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
3kwlA	1	0.9331	100	0.304	Contact Map
3cf4A	2	0.7741	100	0.565	Contact Map
3c8yA	1	0.8954	98.7	0.823	Contact Map
1jflA	2	0.8745	79.1	0.928	Contact Map
2jfnA	1	0.8619	78.4	0.928	Contact Map
3s81A	2	0.8703	77.1	0.929	Contact Map
3qvlA	3	0.8577	74.4	0.931	Contact Map
2gzmA	3	0.4226	70.9	0.932	Contact Map
2jfzA	2	0.41	65.5	0.935	Contact Map
2eq5A	2	0.4268	64.6	0.935	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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