YiaAB - PFAM28P - GREMLIN Contacts

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YiaAB - yiaA/B two helix domain

PFAM:	PF05360	Sequences: FYGQSWASFALALLLLAIGLWNAPLDLWEKGFYAMGLLFLLFSAFTLQKTVRD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (53)
Sequences:	5048 (2148)
Seq/√Len:	295.1
META:	0.842

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_F	48_Q	3.537	1.00
37_L	40_L	3.060	1.00
3_G	7_A	2.333	1.00
25_L	29_E	2.024	1.00
1_F	5_S	1.981	1.00
26_D	29_E	1.910	1.00
16_L	37_L	1.866	1.00
10_A	14_L	1.823	1.00
39_F	42_F	1.676	1.00
2_Y	6_W	1.599	1.00
3_G	6_W	1.584	1.00
7_A	11_L	1.581	1.00
35_M	39_F	1.553	1.00
2_Y	5_S	1.514	1.00
14_L	18_I	1.466	1.00
18_I	22_N	1.390	1.00
47_L	50_T	1.345	1.00
4_Q	8_S	1.342	1.00
8_S	42_F	1.338	1.00
8_S	39_F	1.231	1.00
14_L	21_W	1.231	1.00
20_L	37_L	1.228	1.00
1_F	50_T	1.199	1.00
1_F	4_Q	1.052	1.00
28_W	32_F	1.014	1.00
48_Q	51_V	0.998	1.00
47_L	51_V	0.997	1.00
21_W	27_L	0.997	1.00
17_A	34_A	0.993	1.00
16_L	36_G	0.958	1.00
18_I	27_L	0.944	1.00
49_K	53_D	0.936	1.00
1_F	6_W	0.913	1.00
42_F	46_T	0.908	1.00
45_F	51_V	0.892	1.00
46_T	50_T	0.887	1.00
39_F	43_S	0.863	1.00
11_L	38_L	0.810	1.00
17_A	38_L	0.808	1.00
12_A	16_L	0.788	0.99
17_A	21_W	0.767	0.99
9_F	13_L	0.764	0.99
13_L	37_L	0.763	0.99
7_A	10_A	0.739	0.99
23_A	29_E	0.724	0.99
19_G	32_F	0.715	0.99
15_L	22_N	0.699	0.99
27_L	30_K	0.683	0.98
13_L	40_L	0.679	0.98
38_L	43_S	0.675	0.98
15_L	35_M	0.657	0.98
33_Y	44_A	0.655	0.98
44_A	48_Q	0.651	0.98
25_L	28_W	0.644	0.98
16_L	19_G	0.630	0.97
11_L	14_L	0.629	0.97
26_D	35_M	0.626	0.97
15_L	36_G	0.614	0.97
14_L	27_L	0.613	0.97
13_L	41_L	0.587	0.96
49_K	52_R	0.586	0.96
17_A	27_L	0.581	0.96
41_L	44_A	0.580	0.96
9_F	12_A	0.578	0.96
12_A	15_L	0.576	0.96
6_W	10_A	0.570	0.95
27_L	31_G	0.569	0.95
24_P	28_W	0.565	0.95
8_S	12_A	0.552	0.94
20_L	29_E	0.548	0.94
21_W	24_P	0.536	0.94
21_W	30_K	0.536	0.94
14_L	24_P	0.534	0.93
12_A	37_L	0.529	0.93
6_W	14_L	0.527	0.93
8_S	44_A	0.525	0.93
10_A	21_W	0.511	0.92
4_Q	46_T	0.510	0.92
33_Y	46_T	0.505	0.91
1_F	48_Q	0.500	0.91

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
4lwlA	1	0.5094	5.8	0.845	Contact Map
3bqhA	1	0.5094	2.7	0.869	Contact Map
4hyjA	2	0.9434	2.5	0.871	Contact Map
4od4A	1	1	2.4	0.872	Contact Map
2i68A	2	0.6981	2.3	0.873	Contact Map
3e0mA	4	0.5094	2.2	0.874	Contact Map
4ev6A	3	0.9811	1.9	0.878	Contact Map
5a63B	1	0.3774	1.9	0.878	Contact Map
4gwbA	2	0.4906	1.9	0.878	Contact Map
3b5dA	2	0.9057	1.8	0.881	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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