LsmAD - PFAM28P - GREMLIN Contacts

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LsmAD - LsmAD domain

PFAM:	PF06741	Sequences: FGVKSTYDENLYTTKLDRSSPDYKEREAEAERIAREIEGSASTNAHVAEERGQDDDSGLDEEDKYSAVVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (70)
Sequences:	884 (661)
Seq/√Len:	79.0
META:	0.526

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_E	32_R	3.217	1.00
34_A	38_E	3.113	1.00
22_D	26_R	2.673	1.00
23_Y	26_R	2.617	1.00
25_E	29_E	2.359	1.00
62_E	67_A	2.179	1.00
10_N	15_K	2.178	1.00
27_E	31_E	2.131	1.00
24_K	28_A	1.959	1.00
46_H	49_E	1.945	1.00
31_E	35_R	1.814	1.00
46_H	51_R	1.720	1.00
60_D	63_D	1.624	1.00
32_R	36_E	1.539	0.99
7_Y	11_L	1.493	0.99
44_N	49_E	1.482	0.99
18_R	27_E	1.428	0.99
16_L	20_S	1.414	0.99
3_V	6_T	1.414	0.99
22_D	25_E	1.398	0.99
24_K	27_E	1.374	0.99
44_N	47_V	1.362	0.99
26_R	29_E	1.301	0.98
42_S	48_A	1.272	0.98
17_D	20_S	1.239	0.97
56_D	59_L	1.197	0.97
29_E	33_I	1.192	0.97
59_L	63_D	1.186	0.97
47_V	50_E	1.106	0.95
49_E	65_Y	1.099	0.95
46_H	50_E	1.050	0.93
55_D	64_K	1.048	0.93
1_F	14_T	1.036	0.93
8_D	11_L	1.019	0.92
22_D	27_E	1.012	0.92
20_S	26_R	1.001	0.92
40_S	53_Q	0.972	0.90
25_E	28_A	0.955	0.90
48_A	53_Q	0.943	0.89
13_T	38_E	0.943	0.89
44_N	51_R	0.913	0.87
5_S	11_L	0.901	0.87
35_R	39_G	0.900	0.87
16_L	23_Y	0.868	0.85
44_N	53_Q	0.868	0.85
45_A	64_K	0.858	0.84
42_S	47_V	0.840	0.83
18_R	23_Y	0.831	0.82
34_A	37_I	0.831	0.82
14_T	60_D	0.824	0.81
63_D	67_A	0.819	0.81
63_D	69_V	0.815	0.81
38_E	60_D	0.804	0.80
65_Y	68_V	0.797	0.79
47_V	51_R	0.794	0.79
1_F	20_S	0.773	0.77
23_Y	27_E	0.770	0.77
10_N	16_L	0.759	0.76
54_D	57_S	0.759	0.76
31_E	34_A	0.758	0.76
44_N	48_A	0.747	0.75
53_Q	56_D	0.738	0.74
59_L	64_K	0.732	0.73
42_S	50_E	0.718	0.72
1_F	52_G	0.709	0.71
66_S	70_R	0.705	0.70
21_P	32_R	0.669	0.66
35_R	38_E	0.661	0.65
2_G	13_T	0.659	0.65
1_F	9_E	0.655	0.65
19_S	22_D	0.636	0.62
7_Y	48_A	0.630	0.62
10_N	31_E	0.619	0.60
41_A	57_S	0.618	0.60
49_E	52_G	0.612	0.59
3_V	8_D	0.605	0.58
12_Y	66_S	0.600	0.58
46_H	52_G	0.598	0.58
9_E	13_T	0.594	0.57
19_S	23_Y	0.584	0.56
13_T	16_L	0.584	0.56
28_A	32_R	0.580	0.55
2_G	14_T	0.575	0.55
7_Y	47_V	0.564	0.53
18_R	21_P	0.563	0.53
6_T	40_S	0.562	0.53
51_R	65_Y	0.559	0.53
55_D	58_G	0.559	0.53
47_V	62_E	0.554	0.52
55_D	59_L	0.552	0.52
6_T	11_L	0.550	0.51
49_E	64_K	0.539	0.50
3_V	56_D	0.537	0.50
7_Y	53_Q	0.535	0.50
31_E	38_E	0.529	0.49
46_H	53_Q	0.529	0.49
16_L	21_P	0.512	0.47
13_T	34_A	0.511	0.46
17_D	66_S	0.509	0.46
9_E	14_T	0.506	0.46
28_A	50_E	0.506	0.46
7_Y	27_E	0.505	0.46
46_H	62_E	0.503	0.45
48_A	54_D	0.501	0.45
22_D	66_S	0.500	0.45

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
1wb9A	2	0.5857	5	0.897	Contact Map
3kz5E	2	0.5714	4.6	0.899	Contact Map
1ewqA	2	0.5714	4.2	0.901	Contact Map
1w4rA	3	0.8429	3.5	0.904	Contact Map
2p1mA	1	0.3429	3.1	0.907	Contact Map
2kqrA	1	0.4143	2.9	0.908	Contact Map
4c9bB	1	0.4857	2.8	0.909	Contact Map
4lo0C	1	0.7286	2.7	0.91	Contact Map
1xrsA	2	0.6286	2.6	0.911	Contact Map
3winC	1	0.7286	2.4	0.912	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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