CAAD - PFAM28P - GREMLIN Contacts

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CAAD - CAAD domains of cyanobacterial aminoacyl-tRNA synthetase

PFAM:	PF14159	Sequences: KYLGEFWSQYKKPLTTLGLILAAIVALKLILAVLDAINDIPLLPGLLELVGLGYTGWFVYRYLLFAEDRQELLAKIQSLKKQILG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (83)
Sequences:	1172 (768)
Seq/√Len:	84.3
META:	0.605

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_F	68_D	3.207	1.00
62_Y	71_E	2.707	1.00
10_Y	13_P	2.604	1.00
59_V	63_L	2.346	1.00
54_Y	57_W	2.241	1.00
16_T	20_I	2.214	1.00
56_G	60_Y	2.192	1.00
35_D	39_D	2.043	1.00
56_G	59_V	1.934	1.00
20_I	23_A	1.780	1.00
70_Q	74_A	1.765	1.00
5_E	9_Q	1.757	1.00
43_L	47_L	1.753	1.00
38_N	43_L	1.707	1.00
57_W	62_Y	1.683	1.00
77_Q	81_K	1.675	1.00
27_L	31_L	1.667	1.00
28_K	39_D	1.630	1.00
19_L	23_A	1.609	1.00
73_L	77_Q	1.569	1.00
53_G	57_W	1.558	1.00
4_G	8_S	1.508	0.99
40_I	43_L	1.438	0.99
78_S	82_Q	1.418	0.99
46_L	50_V	1.404	0.99
6_F	10_Y	1.396	0.99
47_L	52_L	1.318	0.99
68_D	71_E	1.307	0.99
26_A	30_I	1.225	0.98
75_K	82_Q	1.192	0.97
26_A	29_L	1.148	0.97
62_Y	72_L	1.127	0.96
75_K	79_L	1.117	0.96
28_K	65_F	1.101	0.96
40_I	44_P	1.101	0.96
14_L	18_G	1.096	0.96
15_T	18_G	1.066	0.95
36_A	39_D	1.051	0.94
24_I	30_I	1.047	0.94
59_V	64_L	1.037	0.94
16_T	43_L	1.017	0.93
54_Y	58_F	0.987	0.92
17_L	25_V	0.963	0.91
34_L	42_L	0.961	0.91
41_P	48_E	0.952	0.91
29_L	65_F	0.949	0.91
29_L	33_V	0.947	0.91
12_K	15_T	0.946	0.91
52_L	56_G	0.927	0.90
58_F	61_R	0.926	0.90
48_E	52_L	0.922	0.89
23_A	27_L	0.920	0.89
80_K	84_L	0.892	0.88
22_A	29_L	0.873	0.87
74_A	77_Q	0.855	0.86
16_T	19_L	0.850	0.85
22_A	32_A	0.834	0.84
21_L	26_A	0.833	0.84
4_G	7_W	0.828	0.84
45_G	48_E	0.822	0.83
8_S	23_A	0.810	0.82
16_T	55_T	0.797	0.81
67_E	75_K	0.795	0.81
17_L	21_L	0.791	0.81
32_A	39_D	0.784	0.80
21_L	40_I	0.781	0.80
7_W	10_Y	0.778	0.80
61_R	71_E	0.771	0.79
15_T	29_L	0.768	0.79
7_W	12_K	0.762	0.78
6_F	9_Q	0.760	0.78
38_N	48_E	0.758	0.78
36_A	54_Y	0.748	0.77
57_W	61_R	0.748	0.77
74_A	85_G	0.745	0.77
56_G	75_K	0.741	0.76
79_L	83_I	0.738	0.76
11_K	14_L	0.733	0.76
23_A	49_L	0.726	0.75
22_A	35_D	0.721	0.74
19_L	22_A	0.720	0.74
46_L	60_Y	0.700	0.72
58_F	69_R	0.696	0.72
45_G	55_T	0.691	0.71
63_L	69_R	0.689	0.71
62_Y	68_D	0.683	0.70
32_A	36_A	0.666	0.68
58_F	64_L	0.651	0.67
34_L	47_L	0.650	0.67
17_L	77_Q	0.649	0.66
76_I	79_L	0.648	0.66
15_T	67_E	0.641	0.66
60_Y	83_I	0.637	0.65
51_G	85_G	0.623	0.63
28_K	32_A	0.619	0.63
5_E	43_L	0.617	0.63
8_S	20_I	0.595	0.60
77_Q	80_K	0.592	0.59
63_L	72_L	0.588	0.59
44_P	48_E	0.587	0.59
17_L	32_A	0.578	0.58
9_Q	12_K	0.573	0.57
53_G	76_I	0.571	0.57
43_L	76_I	0.566	0.56
57_W	70_Q	0.561	0.55
30_I	55_T	0.556	0.55
29_L	60_Y	0.555	0.55
32_A	56_G	0.552	0.54
46_L	83_I	0.542	0.53
75_K	78_S	0.538	0.52
46_L	63_L	0.538	0.52
57_W	71_E	0.536	0.52
24_I	27_L	0.534	0.52
14_L	17_L	0.534	0.52
78_S	83_I	0.524	0.50
7_W	50_V	0.518	0.50
4_G	40_I	0.518	0.50
34_L	74_A	0.515	0.49
14_L	38_N	0.513	0.49
52_L	75_K	0.512	0.49
27_L	64_L	0.511	0.49
18_G	63_L	0.511	0.49
23_A	30_I	0.502	0.48
7_W	16_T	0.500	0.47

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
1ji6A	1	0.6588	32	0.86	Contact Map
2c9kA	1	0.6706	15.8	0.88	Contact Map
1dlcA	1	0.7294	10.7	0.888	Contact Map
1d4aA	2	1	9	0.892	Contact Map
4w8jA	2	0.6235	8.9	0.892	Contact Map
4gi5A	2	1	8.5	0.893	Contact Map
1ciyA	1	0.6706	8.2	0.894	Contact Map
2amjA	2	1	7.6	0.896	Contact Map
3eb7A	2	0.7059	7.1	0.897	Contact Map
4fglA	2	1	4.4	0.906	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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