SPC12 - PFAM28P - GREMLIN Contacts

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SPC12 - Microsomal signal peptidase 12 kDa subunit (SPC12)

PFAM:	PF06645	Sequences: MDFEGQKLAERLYQIILVLFGVIGFIVGYITQDFSLTLYIYLAGVVLTALVVVPPWPFYNRHPLKWLPPKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (69)
Sequences:	778 (599)
Seq/√Len:	72.1
META:	0.411

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_F	44_G	3.727	1.00
16_I	48_T	2.980	1.00
31_T	36_L	2.904	1.00
49_A	53_V	2.803	1.00
4_E	7_K	2.555	1.00
43_A	47_L	2.368	1.00
9_A	52_V	2.056	1.00
4_E	62_H	1.701	1.00
34_F	37_T	1.650	1.00
27_V	36_L	1.641	1.00
55_P	60_N	1.641	1.00
4_E	8_L	1.605	0.99
12_L	16_I	1.594	0.99
26_I	30_I	1.580	0.99
1_M	55_P	1.556	0.99
1_M	34_F	1.489	0.99
5_G	9_A	1.415	0.98
35_S	39_Y	1.400	0.98
27_V	40_I	1.368	0.98
15_I	19_L	1.335	0.98
41_Y	45_V	1.315	0.98
11_R	15_I	1.277	0.97
16_I	51_V	1.248	0.97
24_G	40_I	1.219	0.96
23_I	43_A	1.210	0.96
13_Y	48_T	1.201	0.96
45_V	49_A	1.162	0.95
56_W	63_P	1.147	0.95
38_L	41_Y	1.136	0.94
44_G	55_P	1.074	0.92
56_W	61_R	1.062	0.92
39_Y	51_V	1.046	0.91
42_L	49_A	1.044	0.91
3_F	60_N	1.036	0.91
27_V	31_T	1.016	0.90
28_G	37_T	1.004	0.90
11_R	43_A	0.983	0.89
13_Y	52_V	0.962	0.88
24_G	41_Y	0.952	0.87
44_G	48_T	0.941	0.86
27_V	67_L	0.931	0.86
37_T	41_Y	0.926	0.85
34_F	55_P	0.900	0.84
2_D	5_G	0.879	0.82
13_Y	17_L	0.854	0.81
14_Q	24_G	0.853	0.80
10_E	45_V	0.849	0.80
51_V	58_F	0.845	0.80
26_I	47_L	0.841	0.79
39_Y	43_A	0.828	0.78
39_Y	42_L	0.811	0.77
33_D	41_Y	0.807	0.77
36_L	39_Y	0.790	0.75
33_D	36_L	0.778	0.74
3_F	32_Q	0.775	0.74
5_G	56_W	0.768	0.73
44_G	47_L	0.757	0.72
14_Q	22_V	0.754	0.72
35_S	43_A	0.725	0.69
53_V	58_F	0.717	0.68
18_V	23_I	0.709	0.67
29_Y	36_L	0.704	0.66
14_Q	18_V	0.692	0.65
7_K	69_P	0.687	0.64
4_E	30_I	0.683	0.64
57_P	61_R	0.681	0.64
19_L	26_I	0.657	0.61
14_Q	33_D	0.653	0.61
15_I	20_F	0.653	0.61
30_I	45_V	0.652	0.60
50_L	56_W	0.648	0.60
26_I	65_K	0.643	0.59
26_I	43_A	0.639	0.59
35_S	38_L	0.637	0.59
3_F	55_P	0.633	0.58
3_F	25_F	0.627	0.57
23_I	40_I	0.623	0.57
29_Y	37_T	0.621	0.57
20_F	48_T	0.615	0.56
1_M	37_T	0.607	0.55
21_G	44_G	0.599	0.54
35_S	61_R	0.599	0.54
33_D	57_P	0.588	0.53
22_V	59_Y	0.588	0.53
12_L	59_Y	0.582	0.52
30_I	35_S	0.578	0.52
23_I	57_P	0.569	0.50
13_Y	49_A	0.567	0.50
53_V	69_P	0.566	0.50
1_M	14_Q	0.559	0.49
10_E	13_Y	0.558	0.49
60_N	64_L	0.556	0.49
1_M	4_E	0.549	0.48
50_L	57_P	0.536	0.46
52_V	59_Y	0.531	0.46
59_Y	69_P	0.528	0.45
31_T	39_Y	0.523	0.45
24_G	67_L	0.519	0.44
16_I	34_F	0.518	0.44
11_R	19_L	0.514	0.44
45_V	67_L	0.511	0.43
18_V	69_P	0.506	0.43
7_K	26_I	0.500	0.42
17_L	48_T	0.500	0.42

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
4ev6A	3	0.9155	25.7	0.868	Contact Map
4i0uA	4	0.8873	21	0.873	Contact Map
4uvmA	1	1	15.2	0.881	Contact Map
2a3mA	1	0.169	12.8	0.885	Contact Map
2gfpA	2	1	8.3	0.894	Contact Map
4q65A	1	0.9859	8	0.895	Contact Map
4oh3A	2	0.9859	7.8	0.896	Contact Map
2xq2A	2	0.7887	7.4	0.896	Contact Map
4xnjA	1	0.8873	5.7	0.902	Contact Map
1pw4A	1	0.9014	5.7	0.902	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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