YCIA - ECOLI - GREMLIN Contacts

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YCIA - Acyl-CoA thioester hydrolase YciA

UniProt:	P0A8Z0	Sequences: MSTTHNVPQGDLVLRTLAMPADTNANGDIFGGWLMSQMDIGGAILAKEIAHGRVVTVRVEGMTFLRPVAVGDVVCCYARCVQKGTTSVSINIEVWVKKVASEPIGQRYKATEALFKYVAVDPEGKPRALPVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11121
Length:	132 (118)
Sequences:	3219 (1779)
Seq/√Len:	163.8

ECOLI - YCIA
BACSU - YKHA
HALSA - Q9HR42 Q9HMQ9
SULSO - Q97WD9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_M	115_F	3.435	1.00
85_T	128_A	3.058	1.00
52_G	127_R	2.738	1.00
45_L	78_A	2.674	1.00
42_G	117_Y	2.613	1.00
39_D	56_T	2.508	1.00
35_M	59_V	2.456	1.00
66_R	108_Y	2.352	1.00
23_T	70_V	2.278	1.00
35_M	62_M	2.243	1.00
29_I	34_L	2.172	1.00
75_C	107_R	2.090	1.00
81_V	91_N	2.073	1.00
22_D	33_W	1.903	1.00
82_Q	89_S	1.767	1.00
109_K	112_E	1.740	1.00
121_D	125_K	1.627	1.00
30_F	36_S	1.617	1.00
68_V	110_A	1.603	1.00
18_A	29_I	1.600	1.00
72_D	108_Y	1.599	1.00
16_T	40_I	1.596	1.00
72_D	98_K	1.583	1.00
83_K	129_L	1.542	1.00
96_V	108_Y	1.541	1.00
10_G	49_I	1.513	1.00
33_W	36_S	1.500	1.00
50_A	88_V	1.487	1.00
101_S	105_G	1.431	1.00
98_K	101_S	1.415	1.00
97_K	107_R	1.387	1.00
93_E	109_K	1.360	1.00
58_R	116_K	1.354	1.00
76_C	92_I	1.334	1.00
69_A	72_D	1.319	1.00
48_E	97_K	1.306	1.00
81_V	89_S	1.284	1.00
49_I	80_C	1.280	1.00
55_V	120_V	1.228	1.00
44_I	73_V	1.216	1.00
50_A	54_V	1.212	1.00
89_S	114_L	1.204	1.00
24_N	31_G	1.197	1.00
77_Y	95_W	1.190	1.00
45_L	80_C	1.188	1.00
24_N	30_F	1.163	1.00
68_V	74_V	1.162	1.00
91_N	114_L	1.160	1.00
11_D	77_Y	1.154	1.00
79_R	91_N	1.147	1.00
36_S	40_I	1.139	1.00
13_V	77_Y	1.123	1.00
60_E	114_L	1.117	1.00
22_D	37_Q	1.114	1.00
84_G	87_S	1.103	1.00
72_D	96_V	1.083	1.00
46_A	54_V	1.081	1.00
101_S	106_Q	1.073	0.99
49_I	88_V	1.050	0.99
91_N	112_E	1.043	0.99
80_C	88_V	1.033	0.99
43_A	47_K	1.028	0.99
45_L	90_I	1.009	0.99
87_S	118_V	1.007	0.99
16_T	37_Q	1.005	0.99
26_N	120_V	1.001	0.99
57_V	63_T	0.983	0.99
89_S	116_K	0.974	0.99
95_W	109_K	0.959	0.99
92_I	115_F	0.953	0.99
41_G	78_A	0.938	0.99
95_W	107_R	0.937	0.99
11_D	79_R	0.934	0.99
37_Q	40_I	0.903	0.98
29_I	33_W	0.885	0.98
81_V	114_L	0.866	0.98
38_M	113_A	0.865	0.98
59_V	115_F	0.850	0.97
49_I	83_K	0.850	0.97
69_A	124_G	0.849	0.97
13_V	75_C	0.843	0.97
60_E	116_K	0.842	0.97
34_L	68_V	0.824	0.97
100_A	105_G	0.821	0.97
88_V	129_L	0.812	0.96
120_V	126_P	0.809	0.96
39_D	55_V	0.803	0.96
86_T	126_P	0.802	0.96
34_L	94_V	0.798	0.96
31_G	64_F	0.797	0.96
34_L	111_T	0.790	0.96
45_L	49_I	0.773	0.95
98_K	106_Q	0.771	0.95
98_K	108_Y	0.769	0.95
29_I	37_Q	0.766	0.95
14_L	41_G	0.766	0.95
93_E	112_E	0.763	0.95
80_C	90_I	0.760	0.95
14_L	40_I	0.757	0.95
12_L	45_L	0.756	0.95
52_G	119_A	0.755	0.95
75_C	95_W	0.754	0.95
19_M	25_A	0.753	0.95
41_G	76_C	0.742	0.94
122_P	127_R	0.739	0.94
79_R	93_E	0.726	0.94
60_E	89_S	0.719	0.93
34_L	74_V	0.711	0.93
37_Q	74_V	0.702	0.92
54_V	88_V	0.696	0.92
82_Q	116_K	0.691	0.92
28_D	69_A	0.687	0.92
57_V	87_S	0.686	0.91
37_Q	76_C	0.677	0.91
42_G	92_I	0.675	0.91
23_T	71_G	0.669	0.90
19_M	30_F	0.669	0.90
27_G	71_G	0.661	0.90
51_H	105_G	0.654	0.89
80_C	83_K	0.653	0.89
93_E	114_L	0.646	0.89
43_A	117_Y	0.644	0.89
20_P	116_K	0.641	0.89
121_D	126_P	0.641	0.89
19_M	40_I	0.641	0.89
42_G	115_F	0.639	0.88
40_I	44_I	0.638	0.88
57_V	118_V	0.637	0.88
77_Y	93_E	0.636	0.88
119_A	127_R	0.635	0.88
33_W	37_Q	0.634	0.88
120_V	124_G	0.626	0.87
16_T	62_M	0.622	0.87
73_V	99_V	0.620	0.87
24_N	27_G	0.620	0.87
85_T	126_P	0.615	0.86
50_A	53_R	0.614	0.86
58_R	63_T	0.613	0.86
15_R	18_A	0.611	0.86
55_V	87_S	0.609	0.86
35_M	115_F	0.606	0.86
46_A	90_I	0.605	0.85
54_V	117_Y	0.601	0.85
39_D	84_G	0.601	0.85
21_A	36_S	0.589	0.84
78_A	92_I	0.582	0.83
42_G	90_I	0.579	0.83
29_I	68_V	0.578	0.83
26_N	53_R	0.575	0.83
84_G	118_V	0.572	0.82
49_I	130_P	0.572	0.82
38_M	94_V	0.567	0.82
46_A	117_Y	0.565	0.81
73_V	97_K	0.560	0.81
65_L	82_Q	0.558	0.81
68_V	94_V	0.546	0.79
38_M	92_I	0.545	0.79
56_T	59_V	0.540	0.78
86_T	118_V	0.539	0.78
47_K	99_V	0.538	0.78
123_E	126_P	0.534	0.78
13_V	78_A	0.532	0.77
100_A	122_P	0.530	0.77
28_D	111_T	0.528	0.77
51_H	99_V	0.526	0.77
34_L	59_V	0.524	0.76
49_I	60_E	0.523	0.76
79_R	114_L	0.517	0.75
123_E	128_A	0.515	0.75
38_M	76_C	0.514	0.75
83_K	130_P	0.513	0.75
65_L	112_E	0.513	0.75
64_F	71_G	0.513	0.75
58_R	61_G	0.511	0.75
57_V	111_T	0.511	0.75
98_K	127_R	0.503	0.73
97_K	105_G	0.500	0.73

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
4mobA	3	0.9015	99.9	0.339	Contact Map
4ncpA	5	0.9621	99.9	0.36	Contact Map
4zv3A	3	0.9697	99.9	0.397	Contact Map
1y7uA	5	0.9621	99.8	0.446	Contact Map
2qq2A	5	0.9697	99.8	0.449	Contact Map
2q2bA	5	0.9091	99.8	0.455	Contact Map
1vpmA	5	0.9773	99.8	0.46	Contact Map
2gvhA	3	0.9318	99.8	0.469	Contact Map
3bjkA	5	0.9697	99.8	0.484	Contact Map
4ienA	5	0.9394	99.8	0.495	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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