CitX - PFAM28P - GREMLIN Contacts

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CitX - Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase

PFAM:	PF03802	Sequences: VTLEEILAARERRAARQQELLKRYPLPLVSLTLNIPGPVKNNPLIRRLFEEGLEALEEALKANGIKILEEEELDLATGPEALLVVDADAEELKRLAVEIEESHPLGRLFDIDVLDPDGRPLSRSDLGLPPRKCLLCGEPAKECARSRRHSLEELQAKIEELLEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	164 (162)
Sequences:	1766 (1521)
Seq/√Len:	119.5
META:	0.711

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
138_E	148_R	3.044	1.00
157_K	160_E	3.025	1.00
41_N	46_R	3.020	1.00
138_E	142_E	2.707	1.00
27_P	92_L	2.641	1.00
31_L	52_G	2.576	1.00
157_K	161_L	2.549	1.00
56_L	96_A	2.520	1.00
36_P	158_I	2.501	1.00
57_E	70_E	2.438	1.00
96_A	111_I	2.342	1.00
77_T	80_E	2.246	1.00
3_L	7_L	2.219	1.00
30_S	82_L	2.080	1.00
139_P	142_E	2.001	1.00
5_E	76_A	1.991	1.00
53_L	81_A	1.943	1.00
130_P	139_P	1.933	1.00
52_G	109_F	1.918	1.00
42_N	45_I	1.886	1.00
24_Y	84_V	1.875	1.00
48_L	162_L	1.828	1.00
141_K	144_A	1.826	1.00
16_R	71_E	1.793	1.00
41_N	79_P	1.784	1.00
17_Q	114_L	1.781	1.00
55_A	103_H	1.705	1.00
33_L	48_L	1.699	1.00
134_L	157_K	1.676	1.00
37_G	40_K	1.649	1.00
8_A	12_R	1.618	1.00
33_L	45_I	1.616	1.00
29_V	96_A	1.599	1.00
115_D	119_R	1.554	1.00
87_A	92_L	1.514	1.00
35_I	45_I	1.506	1.00
132_K	137_G	1.456	1.00
90_E	94_R	1.439	1.00
20_L	84_V	1.436	1.00
135_L	157_K	1.427	1.00
56_L	111_I	1.422	1.00
108_L	161_L	1.386	1.00
41_N	74_D	1.353	1.00
34_N	107_R	1.327	1.00
17_Q	28_L	1.323	1.00
29_V	85_V	1.296	1.00
151_L	155_Q	1.293	1.00
14_A	18_Q	1.281	1.00
4_E	8_A	1.253	0.99
57_E	83_L	1.252	0.99
6_I	9_A	1.244	0.99
98_E	102_S	1.230	0.99
9_A	75_L	1.217	0.99
26_L	86_D	1.208	0.99
39_V	155_Q	1.189	0.99
154_L	158_I	1.187	0.99
95_L	98_E	1.183	0.99
12_R	75_L	1.181	0.99
9_A	32_T	1.174	0.99
26_L	68_L	1.169	0.99
67_I	85_V	1.157	0.99
121_L	126_L	1.144	0.99
152_E	156_A	1.141	0.99
53_L	57_E	1.129	0.99
33_L	49_F	1.128	0.99
88_D	91_E	1.104	0.99
19_E	23_R	1.090	0.98
53_L	83_L	1.089	0.98
60_L	85_V	1.085	0.98
31_L	56_L	1.077	0.98
32_T	80_E	1.077	0.98
150_S	153_E	1.074	0.98
26_L	84_V	1.069	0.98
24_Y	69_E	1.064	0.98
31_L	83_L	1.061	0.98
34_N	109_F	1.051	0.98
24_Y	27_P	1.045	0.98
142_E	146_S	1.041	0.98
114_L	120_P	1.037	0.98
59_A	99_I	1.035	0.98
99_I	109_F	1.031	0.98
32_T	77_T	0.997	0.97
31_L	109_F	0.984	0.97
97_V	128_L	0.982	0.97
60_L	95_L	0.976	0.97
45_I	79_P	0.973	0.97
159_E	163_E	0.971	0.97
34_N	37_G	0.965	0.97
122_S	125_D	0.957	0.97
33_L	162_L	0.954	0.96
85_V	92_L	0.953	0.96
74_D	79_P	0.953	0.96
7_L	11_E	0.948	0.96
17_Q	21_L	0.943	0.96
87_A	91_E	0.942	0.96
3_L	11_E	0.938	0.96
65_I	95_L	0.936	0.96
135_L	154_L	0.931	0.96
142_E	148_R	0.929	0.96
119_R	125_D	0.923	0.96
38_P	151_L	0.922	0.96
46_R	79_P	0.914	0.95
155_Q	159_E	0.902	0.95
108_L	134_L	0.900	0.95
96_A	113_V	0.898	0.95
123_R	131_R	0.896	0.95
132_K	139_P	0.887	0.95
92_L	96_A	0.884	0.95
20_L	82_L	0.881	0.94
115_D	118_G	0.870	0.94
49_F	53_L	0.863	0.94
40_K	107_R	0.860	0.94
9_A	80_E	0.860	0.94
9_A	77_T	0.859	0.94
133_C	136_C	0.858	0.94
34_N	40_K	0.851	0.93
16_R	82_L	0.848	0.93
53_L	72_E	0.847	0.93
17_Q	30_S	0.845	0.93
144_A	147_R	0.835	0.93
15_A	19_E	0.832	0.93
147_R	151_L	0.828	0.92
45_I	49_F	0.816	0.92
29_V	56_L	0.814	0.92
35_I	158_I	0.808	0.92
105_L	109_F	0.807	0.91
8_A	11_E	0.798	0.91
9_A	13_R	0.798	0.91
48_L	109_F	0.794	0.91
156_A	160_E	0.791	0.91
28_L	32_T	0.790	0.91
21_L	28_L	0.790	0.91
48_L	105_L	0.788	0.90
72_E	81_A	0.784	0.90
23_R	69_E	0.780	0.90
69_E	84_V	0.778	0.90
29_V	111_I	0.772	0.90
107_R	145_R	0.770	0.89
145_R	148_R	0.767	0.89
65_I	87_A	0.764	0.89
55_A	99_I	0.750	0.88
37_G	107_R	0.748	0.88
49_F	52_G	0.739	0.87
63_N	91_E	0.739	0.87
91_E	94_R	0.737	0.87
28_L	84_V	0.733	0.87
65_I	85_V	0.729	0.87
54_E	58_E	0.724	0.86
55_A	58_E	0.724	0.86
150_S	154_L	0.721	0.86
39_V	42_N	0.711	0.85
21_L	114_L	0.710	0.85
89_A	128_L	0.707	0.85
36_P	134_L	0.706	0.85
59_A	98_E	0.704	0.85
132_K	138_E	0.701	0.85
66_K	86_D	0.699	0.84
134_L	140_A	0.697	0.84
20_L	24_Y	0.695	0.84
39_V	77_T	0.694	0.84
89_A	115_D	0.694	0.84
75_L	80_E	0.691	0.84
13_R	80_E	0.690	0.84
16_R	19_E	0.686	0.83
94_R	98_E	0.686	0.83
102_S	106_G	0.684	0.83
20_L	69_E	0.683	0.83
35_I	49_F	0.683	0.83
17_Q	80_E	0.682	0.83
97_V	126_L	0.682	0.83
14_A	17_Q	0.681	0.83
147_R	150_S	0.680	0.83
132_K	140_A	0.675	0.82
6_I	33_L	0.672	0.82
16_R	73_L	0.670	0.82
38_P	155_Q	0.661	0.81
27_P	84_V	0.660	0.81
20_L	28_L	0.659	0.81
134_L	137_G	0.654	0.80
80_E	114_L	0.654	0.80
107_R	110_D	0.652	0.80
92_L	113_V	0.647	0.80
52_G	111_I	0.644	0.79
144_A	154_L	0.640	0.79
31_L	111_I	0.636	0.78
60_L	92_L	0.633	0.78
110_D	145_R	0.632	0.78
103_H	106_G	0.626	0.77
41_N	45_I	0.625	0.77
37_G	145_R	0.625	0.77
134_L	144_A	0.620	0.77
28_L	82_L	0.603	0.75
143_C	149_H	0.602	0.75
91_E	95_L	0.594	0.74
14_A	147_R	0.594	0.74
27_P	85_V	0.593	0.73
67_I	86_D	0.593	0.73
30_S	80_E	0.590	0.73
17_Q	32_T	0.578	0.72
14_A	120_P	0.577	0.71
140_A	144_A	0.577	0.71
45_I	155_Q	0.576	0.71
10_R	13_R	0.569	0.70
29_V	113_V	0.567	0.70
101_E	132_K	0.567	0.70
93_K	110_D	0.564	0.70
36_P	154_L	0.564	0.70
136_C	143_C	0.562	0.69
52_G	77_T	0.558	0.69
17_Q	77_T	0.556	0.69
7_L	10_R	0.554	0.68
35_I	77_T	0.552	0.68
49_F	74_D	0.550	0.68
103_H	109_F	0.549	0.68
134_L	154_L	0.549	0.68
115_D	121_L	0.548	0.68
44_L	159_E	0.544	0.67
60_L	65_I	0.543	0.67
15_A	18_Q	0.543	0.67
36_P	124_S	0.541	0.67
32_T	114_L	0.538	0.66
134_L	161_L	0.534	0.66
47_R	162_L	0.532	0.65
35_I	40_K	0.530	0.65
6_I	32_T	0.528	0.65
44_L	162_L	0.527	0.65
40_K	77_T	0.527	0.65
39_V	80_E	0.526	0.64
46_R	50_E	0.523	0.64
58_E	90_E	0.522	0.64
97_V	129_P	0.520	0.63
136_C	149_H	0.520	0.63
45_I	154_L	0.519	0.63
50_E	98_E	0.519	0.63
38_P	106_G	0.516	0.63
40_K	145_R	0.513	0.62
32_T	109_F	0.504	0.61
17_Q	20_L	0.504	0.61
30_S	92_L	0.502	0.61
80_E	144_A	0.502	0.61
6_I	77_T	0.502	0.61
11_E	34_N	0.501	0.61
49_F	79_P	0.500	0.61

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
1hc7A	2	0.6768	20.2	0.941	Contact Map
2pt7G	2	0.4512	11.6	0.947	Contact Map
3j65n	1	0.9939	10.8	0.947	Contact Map
3l0iB	1	0.3293	9.2	0.949	Contact Map
1nj1A	2	0.6646	8.9	0.949	Contact Map
3h5nA	3	0.7378	8.6	0.95	Contact Map
4s3qA	1	0.3171	8.5	0.95	Contact Map
2cg8A	4	0.8537	8.2	0.95	Contact Map
2kw0A	1	0.3232	7.4	0.951	Contact Map
1x1nA	2	0.3171	7.1	0.952	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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