YAFJ - ECOLI - GREMLIN Contacts

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YAFJ - Putative glutamine amidotransferase YafJ

UniProt:	Q47147	Sequences: MCELLGMSANVPTDICFSFTGLVQRGGGTGPHKDGWGITFYEGKGCRTFKDPQPSFNSPIAKLVQDYPIKSCSVVAHIRQANRGEVALENTHPFTRELWGRNWTYAHNGQLTGYKSLETGNFRPVGETDSEKAFCWLLHKLTQRYPRTPGNMAAVFKYIASLADELRQKGVFNMLLSDGRYVMAYCSTNLHWITRRAPFGVATLLDQDVEIDFSSQTTPNDVVTVIATQPLTGNETWQKIMPGEWRLFCLGERVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13147
Length:	255 (228)
Sequences:	1616 (981)
Seq/√Len:	65.0

ECOLI - YAFJ
SULSO - Q981E0 Q97XM6 Q97WU1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_T	104_T	9.977	1.00
71_S	74_V	4.804	1.00
241_M	244_E	4.355	1.00
140_K	158_Y	3.582	1.00
75_V	106_A	3.490	1.00
6_G	175_L	3.194	1.00
6_G	182_V	3.078	1.00
77_H	92_H	2.879	1.00
133_A	174_M	2.555	1.00
90_N	126_G	2.548	1.00
124_P	135_C	2.538	1.00
81_A	84_G	2.486	1.00
111_L	133_A	2.424	1.00
184_A	226_I	2.366	1.00
75_V	175_L	2.364	1.00
15_I	38_I	2.342	1.00
126_G	131_E	2.337	1.00
178_D	181_Y	2.305	1.00
95_T	104_T	2.248	1.00
105_Y	174_M	2.099	1.00
15_I	74_V	2.055	1.00
190_L	195_R	2.031	1.00
41_Y	177_S	1.969	1.00
160_A	164_D	1.966	1.00
90_N	131_E	1.958	1.00
90_N	128_T	1.937	1.00
77_H	90_N	1.896	1.00
128_T	131_E	1.892	1.00
63_L	95_T	1.851	1.00
158_Y	162_L	1.850	1.00
106_A	175_L	1.848	1.00
38_I	74_V	1.834	1.00
181_Y	249_C	1.801	1.00
105_Y	134_F	1.762	1.00
224_T	248_F	1.760	1.00
41_Y	104_T	1.688	0.99
194_T	224_T	1.685	0.99
232_T	235_E	1.665	0.99
137_L	152_M	1.658	0.99
226_I	246_R	1.655	0.99
107_H	130_S	1.633	0.99
75_V	177_S	1.600	0.99
4_L	175_L	1.597	0.99
137_L	155_V	1.575	0.99
32_H	78_I	1.564	0.99
240_I	246_R	1.556	0.99
140_K	143_Q	1.535	0.99
103_W	176_L	1.494	0.99
101_R	178_D	1.460	0.98
42_E	47_R	1.453	0.98
49_F	197_A	1.440	0.98
137_L	176_L	1.439	0.98
122_F	142_T	1.405	0.98
55_S	77_H	1.400	0.98
134_F	138_L	1.371	0.97
1_M	5_L	1.369	0.97
94_F	128_T	1.365	0.97
24_Q	28_G	1.354	0.97
16_C	19_F	1.353	0.97
154_A	158_Y	1.330	0.97
133_A	155_V	1.324	0.97
140_K	165_E	1.308	0.97
77_H	106_A	1.306	0.96
155_V	158_Y	1.293	0.96
53_Q	227_A	1.287	0.96
7_M	18_S	1.286	0.96
13_T	17_F	1.257	0.96
102_N	180_R	1.252	0.96
15_I	19_F	1.249	0.95
71_S	177_S	1.245	0.95
16_C	66_D	1.244	0.95
155_V	159_I	1.243	0.95
113_G	116_S	1.234	0.95
194_T	197_A	1.225	0.95
73_S	182_V	1.225	0.95
61_A	231_L	1.210	0.95
47_R	68_P	1.208	0.95
222_V	225_V	1.197	0.94
184_A	245_W	1.189	0.94
139_H	143_Q	1.184	0.94
143_Q	161_S	1.175	0.94
184_A	246_R	1.168	0.94
32_H	56_F	1.128	0.92
72_C	225_V	1.120	0.92
51_D	58_S	1.110	0.92
163_A	174_M	1.108	0.92
69_I	217_T	1.101	0.91
20_T	54_P	1.083	0.91
8_S	73_S	1.081	0.91
96_R	138_L	1.078	0.90
82_N	130_S	1.070	0.90
43_G	70_K	1.068	0.90
41_Y	179_G	1.067	0.90
103_W	128_T	1.065	0.90
190_L	196_R	1.060	0.90
1_M	4_L	1.054	0.89
4_L	106_A	1.034	0.88
217_T	223_V	1.032	0.88
61_A	225_V	1.029	0.88
82_N	110_Q	1.027	0.88
20_T	136_W	1.017	0.88
193_I	242_P	1.012	0.87
189_N	229_Q	1.009	0.87
180_R	249_C	1.003	0.87
112_T	170_G	0.999	0.87
151_N	154_A	0.997	0.87
191_H	194_T	0.989	0.86
179_G	230_P	0.985	0.86
92_H	128_T	0.983	0.86
36_W	40_F	0.971	0.85
29_T	82_N	0.968	0.85
152_M	183_M	0.968	0.85
75_V	182_V	0.967	0.85
59_P	62_K	0.964	0.85
153_A	180_R	0.958	0.84
136_W	162_L	0.954	0.84
191_H	196_R	0.952	0.84
193_I	197_A	0.951	0.84
73_S	177_S	0.949	0.84
120_G	139_H	0.946	0.84
175_L	184_A	0.944	0.83
161_S	165_E	0.943	0.83
152_M	155_V	0.936	0.83
118_E	132_K	0.935	0.83
20_T	24_Q	0.911	0.81
90_N	134_F	0.904	0.81
191_H	239_K	0.902	0.81
181_Y	247_L	0.895	0.80
14_D	17_F	0.889	0.80
35_G	79_R	0.881	0.79
60_I	64_V	0.878	0.79
3_E	9_A	0.878	0.79
155_V	160_A	0.877	0.79
213_F	217_T	0.871	0.78
77_H	126_G	0.871	0.78
228_T	248_F	0.870	0.78
7_M	13_T	0.864	0.78
196_R	222_V	0.859	0.77
29_T	55_S	0.857	0.77
78_I	230_P	0.847	0.76
135_C	173_N	0.845	0.76
40_F	69_I	0.843	0.76
143_Q	154_A	0.842	0.76
47_R	69_I	0.842	0.76
144_R	246_R	0.840	0.76
225_V	231_L	0.835	0.75
62_K	241_M	0.833	0.75
35_G	108_N	0.823	0.74
88_L	183_M	0.822	0.74
72_C	250_L	0.821	0.74
92_H	134_F	0.820	0.74
2_C	5_L	0.808	0.73
45_G	102_N	0.806	0.73
41_Y	178_D	0.799	0.72
10_N	232_T	0.798	0.72
22_L	31_P	0.798	0.72
182_V	248_F	0.795	0.72
188_T	191_H	0.791	0.71
3_E	30_G	0.786	0.71
48_T	95_T	0.786	0.71
144_R	147_R	0.779	0.70
10_N	15_I	0.776	0.70
62_K	66_D	0.775	0.70
15_I	18_S	0.775	0.70
7_M	10_N	0.773	0.69
174_M	185_Y	0.759	0.68
51_D	88_L	0.754	0.68
79_R	108_N	0.750	0.67
180_R	250_L	0.750	0.67
48_T	82_N	0.750	0.67
173_N	227_A	0.747	0.67
62_K	117_L	0.742	0.66
33_K	57_N	0.740	0.66
224_T	227_A	0.739	0.66
188_T	192_W	0.737	0.66
19_F	235_E	0.736	0.66
9_A	21_G	0.733	0.65
116_S	166_L	0.731	0.65
3_E	8_S	0.724	0.64
145_Y	148_T	0.716	0.63
116_S	154_A	0.716	0.63
82_N	171_V	0.713	0.63
83_R	110_Q	0.707	0.63
12_P	17_F	0.703	0.62
41_Y	71_S	0.701	0.62
92_H	131_E	0.699	0.62
49_F	60_I	0.699	0.62
32_H	80_Q	0.697	0.61
5_L	19_F	0.696	0.61
111_L	170_G	0.695	0.61
36_W	54_P	0.694	0.61
2_C	6_G	0.693	0.61
35_G	129_D	0.692	0.61
141_L	173_N	0.689	0.61
57_N	85_E	0.689	0.61
102_N	226_I	0.688	0.60
57_N	148_T	0.688	0.60
52_P	91_T	0.686	0.60
4_L	173_N	0.685	0.60
142_T	146_P	0.685	0.60
9_A	20_T	0.683	0.60
1_M	6_G	0.682	0.60
160_A	169_K	0.682	0.60
157_K	161_S	0.681	0.60
164_D	236_T	0.681	0.60
96_R	135_C	0.676	0.59
3_E	7_M	0.675	0.59
4_L	77_H	0.673	0.59
153_A	157_K	0.671	0.58
91_T	128_T	0.669	0.58
121_N	136_W	0.668	0.58
143_Q	157_K	0.660	0.57
184_A	240_I	0.659	0.57
19_F	61_A	0.655	0.57
126_G	134_F	0.654	0.57
226_I	236_T	0.654	0.57
155_V	176_L	0.653	0.56
79_R	129_D	0.652	0.56
132_K	162_L	0.652	0.56
153_A	183_M	0.649	0.56
30_G	80_Q	0.648	0.56
148_T	236_T	0.648	0.56
40_F	49_F	0.647	0.56
26_G	29_T	0.647	0.56
121_N	229_Q	0.643	0.55
171_V	189_N	0.642	0.55
56_F	78_I	0.642	0.55
10_N	222_V	0.641	0.55
9_A	13_T	0.639	0.55
183_M	247_L	0.639	0.55
42_E	68_P	0.636	0.54
87_A	127_E	0.636	0.54
188_T	193_I	0.631	0.54
5_L	13_T	0.631	0.54
22_L	25_R	0.631	0.54
182_V	249_C	0.631	0.54
102_N	163_A	0.630	0.54
73_S	184_A	0.630	0.54
137_L	141_L	0.627	0.53
81_A	129_D	0.623	0.53
19_F	38_I	0.622	0.53
51_D	91_T	0.620	0.53
59_P	214_S	0.615	0.52
114_Y	134_F	0.615	0.52
91_T	188_T	0.615	0.52
112_T	143_Q	0.614	0.52
137_L	157_K	0.613	0.52
193_I	196_R	0.610	0.51
33_K	91_T	0.609	0.51
120_G	165_E	0.607	0.51
13_T	221_D	0.604	0.51
170_G	173_N	0.603	0.51
21_G	78_I	0.602	0.51
75_V	104_T	0.602	0.51
69_I	137_L	0.599	0.50
32_H	40_F	0.597	0.50
74_V	141_L	0.596	0.50
38_I	61_A	0.592	0.49
152_M	165_E	0.591	0.49
27_G	103_W	0.590	0.49
82_N	85_E	0.590	0.49
102_N	178_D	0.589	0.49
36_W	175_L	0.588	0.49
133_A	159_I	0.586	0.49
21_G	24_Q	0.585	0.49
94_F	105_Y	0.585	0.49
49_F	64_V	0.584	0.48
23_V	33_K	0.583	0.48
157_K	160_A	0.580	0.48
182_V	246_R	0.579	0.48
13_T	19_F	0.576	0.47
12_P	19_F	0.576	0.47
55_S	92_H	0.576	0.47
103_W	137_L	0.573	0.47
240_I	249_C	0.571	0.47
14_D	19_F	0.570	0.47
32_H	36_W	0.569	0.47
75_V	163_A	0.568	0.47
5_L	225_V	0.567	0.46
13_T	157_K	0.565	0.46
12_P	245_W	0.565	0.46
32_H	108_N	0.563	0.46
47_R	71_S	0.563	0.46
41_Y	134_F	0.561	0.46
10_N	70_K	0.560	0.46
80_Q	91_T	0.557	0.45
37_G	93_P	0.557	0.45
23_V	46_C	0.556	0.45
68_P	75_V	0.556	0.45
121_N	169_K	0.555	0.45
36_W	186_C	0.554	0.45
6_G	106_A	0.554	0.45
160_A	187_S	0.553	0.45
127_E	131_E	0.550	0.44
189_N	193_I	0.550	0.44
159_I	168_Q	0.550	0.44
115_K	180_R	0.546	0.44
190_L	194_T	0.546	0.44
22_L	185_Y	0.545	0.44
121_N	142_T	0.545	0.44
20_T	56_F	0.544	0.44
118_E	121_N	0.540	0.43
71_S	91_T	0.540	0.43
156_F	241_M	0.538	0.43
26_G	78_I	0.538	0.43
96_R	102_N	0.537	0.43
61_A	135_C	0.536	0.43
47_R	60_I	0.536	0.43
156_F	236_T	0.534	0.43
40_F	54_P	0.534	0.43
226_I	233_G	0.534	0.43
154_A	159_I	0.534	0.43
196_R	229_Q	0.534	0.43
112_T	240_I	0.534	0.43
13_T	217_T	0.533	0.43
144_R	158_Y	0.532	0.42
18_S	74_V	0.531	0.42
61_A	64_V	0.530	0.42
136_W	140_K	0.526	0.42
187_S	243_G	0.526	0.42
38_I	105_Y	0.525	0.42
31_P	80_Q	0.523	0.41
55_S	90_N	0.522	0.41
105_Y	152_M	0.521	0.41
35_G	81_A	0.521	0.41
55_S	91_T	0.520	0.41
215_S	246_R	0.514	0.40
156_F	172_F	0.513	0.40
66_D	159_I	0.513	0.40
233_G	236_T	0.512	0.40
47_R	88_L	0.512	0.40
112_T	151_N	0.511	0.40
144_R	162_L	0.510	0.40
41_Y	46_C	0.509	0.40
125_V	223_V	0.506	0.39
114_Y	118_E	0.505	0.39
68_P	88_L	0.502	0.39
3_E	228_T	0.502	0.39
124_P	247_L	0.501	0.39
46_C	229_Q	0.501	0.39
197_A	239_K	0.500	0.39
49_F	59_P	0.500	0.39

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
3mdnA	4	0.8039	100	0.417	Contact Map
1te5A	2	0.9882	100	0.434	Contact Map
4zflA	5	0.8275	100	0.473	Contact Map
4amvA	2	0.8235	100	0.59	Contact Map
1xffA	2	0.8235	100	0.611	Contact Map
1ao0A	3	0.8275	100	0.621	Contact Map
1ecfA	4	0.8902	100	0.626	Contact Map
1ea0A	1	0.8745	99.9	0.71	Contact Map
1ofdA	1	0.8667	99.8	0.724	Contact Map
1jgtA	2	0.6902	99.7	0.752	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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