YAAB - BACSU - GREMLIN Contacts

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YAAB - Uncharacterized protein YaaB

UniProt:	P37525	Sequences: MYIHLGDDFVVSTRDIVGIFDFKANMSPIVEEFLKKQKHKVVPSVNGTPKSIVVTVQNIYYSPLSSSTLKKRAQFMFEIDS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	81 (76)
Sequences:	240 (171)
Seq/√Len:	19.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_D	63_P	3.366	1.00
5_L	44_S	2.891	0.99
22_F	52_I	2.752	0.98
3_I	13_T	2.579	0.98
55_T	63_P	2.536	0.97
2_Y	65_S	2.047	0.91
32_E	47_G	2.034	0.91
71_K	74_Q	1.885	0.87
26_M	61_Y	1.710	0.82
35_K	59_I	1.706	0.82
28_P	61_Y	1.632	0.78
19_I	69_L	1.588	0.77
60_Y	63_P	1.526	0.74
33_F	39_H	1.488	0.72
4_H	62_S	1.487	0.72
30_V	37_Q	1.450	0.70
9_F	46_N	1.444	0.69
7_D	44_S	1.410	0.67
29_I	32_E	1.379	0.66
12_S	39_H	1.336	0.63
54_V	58_N	1.297	0.61
10_V	75_F	1.263	0.59
16_I	43_P	1.235	0.57
53_V	71_K	1.225	0.56
3_I	73_A	1.201	0.55
15_D	71_K	1.187	0.54
4_H	69_L	1.185	0.54
8_D	45_V	1.176	0.53
5_L	11_V	1.162	0.52
2_Y	45_V	1.161	0.52
8_D	17_V	1.107	0.49
15_D	57_Q	1.103	0.48
13_T	66_S	1.094	0.48
8_D	73_A	1.064	0.46
18_G	63_P	1.055	0.45
2_Y	67_S	1.050	0.45
17_V	57_Q	1.041	0.44
47_G	60_Y	1.034	0.44
10_V	27_S	1.020	0.43
67_S	71_K	1.017	0.43
3_I	70_K	0.985	0.41
19_I	66_S	0.977	0.40
36_K	40_K	0.973	0.40
42_V	58_N	0.966	0.40
4_H	55_T	0.955	0.39
49_P	61_Y	0.946	0.39
16_I	67_S	0.934	0.38
17_V	34_L	0.930	0.38
55_T	62_S	0.924	0.37
44_S	64_L	0.923	0.37
16_I	32_E	0.919	0.37
44_S	63_P	0.919	0.37
49_P	52_I	0.909	0.36
52_I	61_Y	0.906	0.36
23_K	34_L	0.883	0.35
15_D	58_N	0.877	0.34
20_F	63_P	0.873	0.34
55_T	60_Y	0.861	0.34
23_K	48_T	0.853	0.33
48_T	64_L	0.849	0.33
13_T	16_I	0.847	0.33
3_I	69_L	0.820	0.31
18_G	55_T	0.819	0.31
3_I	57_Q	0.807	0.30
15_D	48_T	0.802	0.30
20_F	52_I	0.798	0.30
35_K	47_G	0.791	0.30
16_I	48_T	0.775	0.29
33_F	66_S	0.768	0.28
5_L	45_V	0.766	0.28
23_K	30_V	0.764	0.28
22_F	71_K	0.742	0.27
24_A	63_P	0.735	0.27
40_K	56_V	0.734	0.27
12_S	16_I	0.732	0.27
47_G	61_Y	0.702	0.25
14_R	30_V	0.692	0.25
4_H	65_S	0.686	0.24
34_L	61_Y	0.674	0.24
3_I	12_S	0.672	0.24
5_L	60_Y	0.664	0.23
28_P	46_N	0.661	0.23
18_G	41_V	0.658	0.23
10_V	59_I	0.658	0.23
41_V	54_V	0.651	0.23
28_P	45_V	0.639	0.22
7_D	73_A	0.619	0.21
33_F	64_L	0.618	0.21
48_T	61_Y	0.610	0.21
43_P	67_S	0.608	0.21
7_D	64_L	0.600	0.20
36_K	39_H	0.597	0.20
43_P	61_Y	0.595	0.20
31_E	37_Q	0.591	0.20
2_Y	29_I	0.590	0.20
22_F	49_P	0.584	0.20
7_D	61_Y	0.582	0.20
27_S	65_S	0.578	0.20
27_S	60_Y	0.570	0.19
25_N	49_P	0.561	0.19
30_V	41_V	0.559	0.19
30_V	34_L	0.555	0.19
16_I	52_I	0.552	0.19
8_D	57_Q	0.544	0.18
67_S	75_F	0.537	0.18
36_K	56_V	0.529	0.18
42_V	57_Q	0.524	0.17
23_K	49_P	0.516	0.17
32_E	40_K	0.513	0.17
16_I	24_A	0.511	0.17
18_G	52_I	0.506	0.17
16_I	58_N	0.505	0.17
40_K	45_V	0.504	0.17
10_V	23_K	0.500	0.17

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
3sooA	2	0.3827	11.5	0.919	Contact Map
4yivA	1	0.9877	8.6	0.924	Contact Map
2jrbA	1	0.2222	6.9	0.927	Contact Map
2ykoA	3	0.9259	5.9	0.929	Contact Map
2kkuA	1	0.9259	5.1	0.931	Contact Map
2x2zA	1	0.9877	4.5	0.933	Contact Map
3pg7A	1	0.9753	4.3	0.934	Contact Map
4apmA	1	0.8395	4.2	0.934	Contact Map
4nexA	2	0.2222	4.1	0.934	Contact Map
4xttA	2	0.4074	3.9	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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