TRAM1 - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

TRAM1 - TRAM1-like protein

PFAM:	PF08390	Sequences: TSKFIFLSYPVPDYPPETGLYGKGPKDLAFVFFYIVVFTFLRAFIMEYVLRPLARRLGISKRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	63 (61)
Sequences:	979 (664)
Seq/√Len:	85.0
META:	0.309

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_Y	24_G	6.755	1.00
3_K	26_K	3.849	1.00
26_K	29_A	2.863	1.00
45_I	49_V	2.484	1.00
9_Y	22_G	2.121	1.00
45_I	50_L	1.726	1.00
43_A	46_M	1.651	1.00
32_F	35_I	1.629	1.00
10_P	19_G	1.624	1.00
8_S	30_F	1.619	1.00
30_F	34_Y	1.356	0.99
39_T	46_M	1.277	0.98
53_L	57_L	1.270	0.98
46_M	51_R	1.261	0.98
40_F	44_F	1.259	0.98
39_T	43_A	1.259	0.98
7_L	21_Y	1.250	0.98
44_F	48_Y	1.229	0.98
3_K	29_A	1.222	0.98
13_D	17_E	1.184	0.97
59_I	62_R	1.151	0.97
28_L	32_F	1.133	0.96
4_F	32_F	1.118	0.96
51_R	55_R	1.115	0.96
23_K	43_A	1.096	0.96
13_D	16_P	1.060	0.95
2_S	9_Y	1.037	0.94
31_V	51_R	1.033	0.94
14_Y	17_E	0.975	0.92
4_F	48_Y	0.968	0.92
14_Y	19_G	0.962	0.91
23_K	40_F	0.924	0.90
43_A	48_Y	0.900	0.89
14_Y	18_T	0.891	0.88
42_R	52_P	0.888	0.88
52_P	58_G	0.876	0.87
31_V	38_F	0.873	0.87
23_K	28_L	0.871	0.87
23_K	38_F	0.863	0.86
57_L	60_S	0.862	0.86
23_K	29_A	0.847	0.85
15_P	18_T	0.833	0.84
39_T	45_I	0.826	0.84
32_F	36_V	0.826	0.84
31_V	54_A	0.813	0.83
50_L	53_L	0.807	0.82
43_A	47_E	0.807	0.82
5_I	41_L	0.780	0.80
57_L	62_R	0.768	0.79
7_L	37_V	0.754	0.78
34_Y	37_V	0.748	0.77
17_E	25_P	0.746	0.77
6_F	34_Y	0.730	0.76
15_P	41_L	0.725	0.75
21_Y	41_L	0.710	0.74
5_I	37_V	0.708	0.73
16_P	19_G	0.701	0.73
30_F	42_R	0.696	0.72
46_M	52_P	0.690	0.71
44_F	51_R	0.687	0.71
39_T	42_R	0.681	0.70
44_F	62_R	0.679	0.70
38_F	41_L	0.672	0.69
31_V	57_L	0.664	0.69
2_S	6_F	0.642	0.66
2_S	35_I	0.637	0.65
3_K	10_P	0.627	0.64
11_V	22_G	0.617	0.63
42_R	54_A	0.597	0.60
8_S	29_A	0.596	0.60
25_P	28_L	0.590	0.59
12_P	19_G	0.583	0.59
5_I	33_F	0.569	0.57
10_P	16_P	0.568	0.57
4_F	55_R	0.567	0.56
46_M	50_L	0.564	0.56
18_T	22_G	0.557	0.55
4_F	29_A	0.555	0.55
38_F	54_A	0.550	0.54
19_G	25_P	0.548	0.54
7_L	53_L	0.546	0.54
48_Y	55_R	0.540	0.53
25_P	36_V	0.536	0.52
53_L	56_R	0.535	0.52
12_P	16_P	0.530	0.52
4_F	26_K	0.519	0.50
30_F	41_L	0.517	0.50
28_L	31_V	0.513	0.49
42_R	46_M	0.507	0.48
36_V	39_T	0.506	0.48
30_F	52_P	0.503	0.48
51_R	60_S	0.500	0.48

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
3l9dA	1	0.0159	5.4	0.888	Contact Map
2vpzA	1	1	3.2	0.9	Contact Map
2e7zA	1	0.9683	2.8	0.903	Contact Map
2iv2X	1	1	2.7	0.904	Contact Map
2lf8A	1	0.5238	2.7	0.904	Contact Map
3l15A	1	0.6667	2.6	0.905	Contact Map
1awcA	1	0.4603	2.5	0.905	Contact Map
4ojdH	3	0.1429	2.4	0.907	Contact Map
2ed2A	1	0.4762	2.2	0.908	Contact Map
2napA	1	1	2.1	0.91	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.

Page generated in 0.0045 seconds.