SRP40_C - PFAM28P - GREMLIN Contacts

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SRP40_C - SRP40, C-terminal domain

PFAM:	PF05022	Sequences: PFQRVDPEEWVVFVDPRLADNSYEAKGGGGDDYGAKANEDLIVTRGKGFRKEKTKKKRGSYRGGAIDTQSVNSIKF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (76)
Sequences:	611 (398)
Seq/√Len:	45.7
META:	0.468

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_R	54_T	4.071	1.00
6_D	9_E	3.732	1.00
44_T	48_G	3.716	1.00
38_N	42_I	3.334	1.00
51_K	54_T	3.116	1.00
40_D	56_K	3.012	1.00
16_P	19_A	2.411	1.00
52_E	56_K	2.145	1.00
17_R	74_I	1.994	0.99
23_Y	32_D	1.961	0.99
20_D	25_A	1.738	0.98
31_D	35_A	1.641	0.97
35_A	39_E	1.637	0.97
56_K	59_G	1.521	0.96
40_D	43_V	1.433	0.94
47_K	54_T	1.319	0.91
29_G	32_D	1.312	0.91
37_A	62_R	1.278	0.90
37_A	59_G	1.233	0.88
26_K	72_N	1.216	0.87
45_R	48_G	1.215	0.87
33_Y	59_G	1.194	0.86
32_D	67_D	1.184	0.86
23_Y	53_K	1.160	0.85
69_Q	72_N	1.135	0.84
71_V	74_I	1.125	0.83
12_V	15_D	1.123	0.83
59_G	62_R	1.120	0.83
23_Y	28_G	1.117	0.83
37_A	61_Y	1.110	0.82
60_S	63_G	1.097	0.81
31_D	34_G	1.069	0.80
43_V	48_G	1.017	0.76
22_S	25_A	1.004	0.75
67_D	70_S	0.981	0.74
33_Y	54_T	0.968	0.73
37_A	63_G	0.968	0.73
33_Y	60_S	0.956	0.72
33_Y	72_N	0.955	0.71
48_G	51_K	0.932	0.70
14_V	74_I	0.914	0.68
30_G	39_E	0.907	0.68
40_D	44_T	0.885	0.66
23_Y	35_A	0.879	0.65
48_G	52_E	0.865	0.64
24_E	38_N	0.855	0.63
68_T	71_V	0.855	0.63
52_E	58_R	0.842	0.62
28_G	32_D	0.838	0.61
30_G	35_A	0.819	0.60
15_D	18_L	0.802	0.58
36_K	60_S	0.775	0.55
32_D	51_K	0.767	0.55
56_K	61_Y	0.765	0.54
32_D	43_V	0.757	0.54
61_Y	64_G	0.749	0.53
23_Y	26_K	0.744	0.52
7_P	10_W	0.734	0.51
7_P	13_F	0.725	0.50
66_I	72_N	0.725	0.50
47_K	50_R	0.724	0.50
69_Q	74_I	0.722	0.50
34_G	72_N	0.720	0.50
2_F	5_V	0.717	0.50
68_T	74_I	0.711	0.49
3_Q	6_D	0.707	0.49
31_D	65_A	0.706	0.49
50_R	56_K	0.706	0.49
56_K	60_S	0.694	0.47
12_V	16_P	0.683	0.46
34_G	75_K	0.669	0.45
11_V	14_V	0.669	0.45
12_V	68_T	0.666	0.45
8_E	69_Q	0.663	0.44
41_L	52_E	0.663	0.44
3_Q	8_E	0.660	0.44
51_K	56_K	0.646	0.43
2_F	6_D	0.644	0.43
25_A	31_D	0.644	0.43
13_F	19_A	0.638	0.42
3_Q	14_V	0.635	0.42
11_V	15_D	0.633	0.42
39_E	43_V	0.624	0.41
25_A	76_F	0.620	0.40
24_E	42_I	0.608	0.39
3_Q	45_R	0.593	0.38
16_P	45_R	0.591	0.38
52_E	63_G	0.586	0.37
59_G	64_G	0.582	0.37
7_P	38_N	0.580	0.37
37_A	56_K	0.579	0.36
7_P	12_V	0.575	0.36
5_V	18_L	0.575	0.36
26_K	29_G	0.572	0.36
41_L	63_G	0.551	0.34
1_P	33_Y	0.550	0.34
15_D	19_A	0.548	0.34
24_E	30_G	0.548	0.34
70_S	75_K	0.544	0.33
32_D	35_A	0.540	0.33
60_S	66_I	0.539	0.33
29_G	35_A	0.530	0.32
26_K	45_R	0.530	0.32
46_G	55_K	0.526	0.32
47_K	69_Q	0.523	0.32
9_E	19_A	0.521	0.31
37_A	64_G	0.520	0.31
8_E	15_D	0.519	0.31
64_G	75_K	0.518	0.31
11_V	17_R	0.513	0.31
14_V	18_L	0.510	0.30
12_V	17_R	0.506	0.30
13_F	16_P	0.506	0.30
2_F	38_N	0.500	0.30

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
4nfnA	1	0.4605	4	0.92	Contact Map
3j7aH	1	0.9737	2.1	0.931	Contact Map
3tr7A	1	0.2895	2	0.931	Contact Map
4mveA	1	0.4079	2	0.932	Contact Map
1wxrA	1	0.8026	1.7	0.934	Contact Map
4btkA	1	0.4211	1.5	0.936	Contact Map
3gkuA	2	0.1579	1.4	0.938	Contact Map
4bpeY	1	0.9737	1.4	0.938	Contact Map
3j60G	1	0.9737	1.3	0.938	Contact Map
3cueA	1	0.3421	1.3	0.939	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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