Sensor_TM1 - PFAM28P - GREMLIN Contacts

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Sensor_TM1 - Sensor N-terminal transmembrane domain

PFAM:	PF13755	Sequences: RRGLVSLRFSSLTRRILALNLLALAVLVAGILYLNQFRAGLIDARVQSLVTQAEIIAGAIAAQASATVDTDLITIDP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (67)
Sequences:	2869 (1429)
Seq/√Len:	174.5
META:	0.92

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_D	72_L	2.851	1.00
23_A	27_L	2.595	1.00
10_S	14_R	2.349	1.00
48_S	52_Q	2.192	1.00
11_S	15_R	2.158	1.00
36_Q	39_A	1.988	1.00
19_L	45_R	1.976	1.00
33_Y	37_F	1.918	1.00
11_S	14_R	1.887	1.00
65_S	72_L	1.815	1.00
39_A	43_D	1.804	1.00
22_L	25_A	1.739	1.00
45_R	56_I	1.734	1.00
4_L	7_L	1.573	1.00
67_T	70_T	1.544	1.00
28_V	31_I	1.543	1.00
68_V	71_D	1.441	1.00
5_V	9_F	1.357	1.00
8_R	35_N	1.351	1.00
19_L	27_L	1.337	1.00
65_S	69_D	1.334	1.00
9_F	28_V	1.307	1.00
50_V	54_E	1.276	1.00
67_T	71_D	1.249	1.00
55_I	58_G	1.201	1.00
42_I	46_V	1.175	1.00
16_I	20_N	1.097	1.00
52_Q	55_I	1.081	1.00
32_L	35_N	1.060	1.00
20_N	27_L	1.059	1.00
65_S	71_D	1.052	1.00
51_T	54_E	1.049	1.00
31_I	35_N	1.048	1.00
35_N	46_V	1.039	0.99
43_D	47_Q	1.038	0.99
46_V	57_A	1.032	0.99
10_S	32_L	1.005	0.99
16_I	38_R	0.973	0.99
25_A	36_Q	0.956	0.99
9_F	13_T	0.926	0.99
53_A	57_A	0.925	0.99
5_V	8_R	0.925	0.99
16_I	27_L	0.898	0.98
49_L	53_A	0.890	0.98
12_L	16_I	0.888	0.98
54_E	58_G	0.887	0.98
46_V	51_T	0.868	0.98
18_A	33_Y	0.857	0.98
68_V	72_L	0.856	0.98
62_A	65_S	0.816	0.97
38_R	45_R	0.810	0.97
19_L	23_A	0.806	0.97
45_R	52_Q	0.806	0.97
8_R	18_A	0.804	0.97
4_L	47_Q	0.792	0.97
19_L	37_F	0.774	0.96
23_A	47_Q	0.771	0.96
24_L	60_I	0.761	0.96
11_S	36_Q	0.751	0.95
9_F	21_L	0.746	0.95
13_T	19_L	0.738	0.95
57_A	61_A	0.736	0.95
65_S	70_T	0.732	0.95
37_F	46_V	0.732	0.95
7_L	29_A	0.725	0.94
29_A	67_T	0.719	0.94
66_A	70_T	0.704	0.94
29_A	32_L	0.699	0.93
46_V	56_I	0.677	0.92
58_G	62_A	0.673	0.92
44_A	56_I	0.672	0.92
30_G	49_L	0.665	0.92
15_R	57_A	0.656	0.91
65_S	68_V	0.654	0.91
34_L	72_L	0.635	0.90
31_I	39_A	0.632	0.89
9_F	14_R	0.610	0.88
47_Q	71_D	0.597	0.87
15_R	44_A	0.597	0.87
31_I	41_L	0.593	0.86
44_A	48_S	0.591	0.86
40_G	44_A	0.582	0.85
16_I	45_R	0.572	0.84
66_A	72_L	0.571	0.84
52_Q	57_A	0.569	0.84
18_A	28_V	0.562	0.83
35_N	40_G	0.560	0.83
4_L	8_R	0.553	0.82
31_I	62_A	0.552	0.82
62_A	71_D	0.550	0.82
15_R	18_A	0.540	0.81
32_L	39_A	0.527	0.79
50_V	57_A	0.523	0.78
6_S	21_L	0.515	0.77
21_L	28_V	0.514	0.77
42_I	56_I	0.512	0.77
27_L	53_A	0.509	0.77
19_L	51_T	0.508	0.76
19_L	31_I	0.502	0.76
15_R	33_Y	0.500	0.75

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
4cq4A	4	0	31.6	0.845	Contact Map
3e4oA	2	0.4545	28.2	0.849	Contact Map
3cwfA	2	0.5065	21.5	0.857	Contact Map
2kseA	1	0.4805	12.9	0.871	Contact Map
2w3zA	1	0.039	9.9	0.878	Contact Map
2mj6A	1	0.5584	7.6	0.884	Contact Map
4k0jA	3	0.9221	2.8	0.905	Contact Map
3cuqA	1	0.3766	2.7	0.906	Contact Map
4akkA	2	0.6753	2.4	0.908	Contact Map
4k08A	2	0.4935	2.2	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.

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