TPPK_C - PFAM28P - GREMLIN Contacts

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TPPK_C - Thiamine pyrophosphokinase C terminal

PFAM:	PF12555	Sequences: KGVSRLYRSRVSGWPLLLLVLAALVALVVAVAVSPAGRDLLDLLWLRLRDLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (51)
Sequences:	4136 (2180)
Seq/√Len:	305.3
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_S	15_P	3.450	1.00
2_G	5_R	2.867	1.00
31_V	37_G	2.325	1.00
23_A	26_A	2.129	1.00
28_V	32_A	1.943	1.00
43_L	47_R	1.914	1.00
39_D	43_L	1.839	1.00
2_G	7_Y	1.751	1.00
45_W	49_R	1.610	1.00
34_S	37_G	1.557	1.00
38_R	41_L	1.470	1.00
11_V	19_L	1.458	1.00
13_G	17_L	1.399	1.00
3_V	6_L	1.375	1.00
48_L	51_L	1.323	1.00
47_R	50_D	1.306	1.00
1_K	4_S	1.288	1.00
24_L	28_V	1.285	1.00
26_A	29_V	1.216	1.00
46_L	50_D	1.215	1.00
25_V	29_V	1.174	1.00
39_D	42_D	1.091	1.00
40_L	43_L	1.088	1.00
10_R	14_W	1.073	1.00
11_V	15_P	1.022	1.00
19_L	22_A	1.016	1.00
42_D	46_L	0.979	1.00
16_L	22_A	0.969	1.00
20_V	34_S	0.942	1.00
8_R	11_V	0.940	1.00
46_L	49_R	0.938	1.00
30_A	37_G	0.936	1.00
7_Y	25_V	0.932	1.00
1_K	5_R	0.927	1.00
18_L	25_V	0.913	1.00
19_L	23_A	0.868	1.00
47_R	51_L	0.858	1.00
45_W	48_L	0.857	1.00
4_S	8_R	0.854	1.00
33_V	36_A	0.822	1.00
42_D	45_W	0.788	1.00
30_A	36_A	0.765	0.99
30_A	44_L	0.728	0.99
31_V	35_P	0.728	0.99
23_A	27_L	0.713	0.99
19_L	39_D	0.698	0.99
14_W	21_L	0.692	0.99
9_S	12_S	0.689	0.99
17_L	21_L	0.681	0.99
5_R	16_L	0.675	0.98
4_S	9_S	0.663	0.98
21_L	26_A	0.662	0.98
4_S	47_R	0.654	0.98
19_L	26_A	0.649	0.98
34_S	42_D	0.631	0.98
20_V	24_L	0.628	0.98
23_A	30_A	0.624	0.97
27_L	34_S	0.604	0.97
2_G	38_R	0.591	0.97
17_L	20_V	0.589	0.96
29_V	33_V	0.579	0.96
15_P	23_A	0.576	0.96
4_S	7_Y	0.567	0.96
41_L	44_L	0.567	0.96
1_K	49_R	0.564	0.95
10_R	15_P	0.562	0.95
1_K	36_A	0.556	0.95
41_L	45_W	0.543	0.94
26_A	33_V	0.530	0.94
43_L	46_L	0.527	0.94
14_W	26_A	0.517	0.93
32_A	38_R	0.514	0.93
20_V	23_A	0.514	0.93
14_W	35_P	0.510	0.92
21_L	31_V	0.502	0.92
14_W	17_L	0.500	0.92

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
3ixzA	1	1	11.7	0.804	Contact Map
3tx3A	2	0.7692	10.2	0.808	Contact Map
2m8rA	1	0.7308	9.8	0.81	Contact Map
3ar4A	1	1	9.4	0.811	Contact Map
2zxeA	1	0.9615	5.8	0.829	Contact Map
4pd6A	3	0.9808	4.9	0.835	Contact Map
3ux4A	3	1	2.2	0.862	Contact Map
4c7rA	3	0.8269	1.8	0.868	Contact Map
3gzfA	2	0.3462	1.7	0.869	Contact Map
2wswA	3	0.8269	1.7	0.869	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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