TMA7 - PFAM28P - GREMLIN Contacts

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TMA7 - Translation machinery associated TMA7

PFAM:	PF09072	Sequences: GRQGGKKKPLKAPKKEKKELDEDDLAFKQKQKEEQKALKELAAKAAGKGPLGGGGIKKSGKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (62)
Sequences:	560 (312)
Seq/√Len:	39.6
META:	0.436

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_F	31_Q	3.836	1.00
29_Q	32_K	3.384	1.00
29_Q	33_E	2.980	1.00
36_K	40_E	2.357	1.00
33_E	37_A	2.329	1.00
39_K	42_A	2.145	0.99
20_L	28_K	1.954	0.99
31_Q	35_Q	1.767	0.97
39_K	43_A	1.665	0.96
28_K	31_Q	1.640	0.96
51_L	56_I	1.594	0.95
26_A	29_Q	1.572	0.95
20_L	25_L	1.493	0.93
38_L	42_A	1.486	0.93
42_A	46_A	1.410	0.91
56_I	59_S	1.408	0.91
34_E	38_L	1.380	0.90
25_L	29_Q	1.348	0.89
38_L	41_L	1.320	0.88
3_Q	7_K	1.312	0.88
45_A	49_G	1.287	0.87
32_K	35_Q	1.280	0.86
20_L	24_D	1.217	0.83
38_L	45_A	1.183	0.81
36_K	39_K	1.157	0.80
40_E	44_K	1.133	0.79
51_L	59_S	1.113	0.77
43_A	46_A	1.082	0.75
41_L	52_G	1.077	0.75
7_K	12_A	1.074	0.75
35_Q	39_K	1.070	0.74
23_D	26_A	1.062	0.74
12_A	15_K	1.045	0.73
33_E	36_K	0.987	0.68
41_L	44_K	0.975	0.67
32_K	36_K	0.963	0.66
37_A	40_E	0.952	0.65
40_E	43_A	0.929	0.64
55_G	59_S	0.920	0.63
41_L	51_L	0.917	0.62
47_G	53_G	0.860	0.58
3_Q	36_K	0.852	0.57
35_Q	38_L	0.827	0.55
55_G	58_K	0.800	0.52
53_G	58_K	0.794	0.52
50_P	56_I	0.756	0.48
33_E	40_E	0.745	0.47
51_L	54_G	0.738	0.46
2_R	47_G	0.728	0.46
4_G	7_K	0.721	0.45
1_G	31_Q	0.717	0.45
44_K	49_G	0.711	0.44
7_K	33_E	0.685	0.42
35_Q	43_A	0.681	0.41
24_D	58_K	0.671	0.40
13_P	39_K	0.669	0.40
5_G	8_K	0.665	0.40
16_E	47_G	0.663	0.40
2_R	15_K	0.658	0.39
2_R	32_K	0.655	0.39
31_Q	34_E	0.654	0.39
19_E	23_D	0.622	0.36
5_G	11_K	0.621	0.36
13_P	36_K	0.616	0.36
56_I	60_G	0.613	0.35
16_E	23_D	0.610	0.35
17_K	20_L	0.608	0.35
34_E	37_A	0.598	0.34
7_K	15_K	0.598	0.34
16_E	25_L	0.583	0.33
17_K	34_E	0.582	0.33
2_R	7_K	0.576	0.32
57_K	61_K	0.576	0.32
23_D	27_F	0.574	0.32
35_Q	40_E	0.564	0.31
22_E	25_L	0.560	0.31
18_K	40_E	0.556	0.31
1_G	17_K	0.555	0.31
8_K	11_K	0.553	0.31
32_K	42_A	0.549	0.30
1_G	7_K	0.548	0.30
28_K	32_K	0.543	0.30
26_A	46_A	0.539	0.30
30_K	54_G	0.536	0.29
47_G	51_L	0.531	0.29
18_K	28_K	0.529	0.29
42_A	50_P	0.527	0.29
46_A	49_G	0.524	0.28
18_K	44_K	0.516	0.28
12_A	37_A	0.514	0.28
42_A	58_K	0.514	0.28
17_K	25_L	0.513	0.28
14_K	22_E	0.500	0.27

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
1ou0A	4	0.3226	1.7	0.916	Contact Map
1f2vA	2	0.3387	1.7	0.917	Contact Map
3e7dA	2	0.3065	1.7	0.917	Contact Map
4au1A	2	0.3387	1.6	0.918	Contact Map
1jjrA	1	0	1.5	0.919	Contact Map
3avrB	1	0.2581	1.3	0.923	Contact Map
3p9dH	1	0	1	0.928	Contact Map
3izsv	1	0	0.9	0.929	Contact Map
4cj9A	1	0	0.9	0.93	Contact Map
3i44A	2	0.3387	0.9	0.93	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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