BofA - PFAM28P - GREMLIN Contacts

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BofA - SigmaK-factor processing regulatory protein BofA

PFAM:	PF07441	Sequences: IGLLLLLLILKLLLKPLKLLLKLLINAVLGLVLLFLVNLLGGFFGLHIPINPITALIVGILGIPGVILLILLKLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (73)
Sequences:	3704 (2803)
Seq/√Len:	328.0
META:	0.812

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_V	66_V	3.432	1.00
58_V	66_V	3.423	1.00
51_N	54_T	2.906	1.00
41_G	44_F	2.454	1.00
57_I	65_G	2.341	1.00
30_G	59_G	2.101	1.00
10_L	14_L	2.038	1.00
34_L	50_I	1.944	1.00
7_L	11_K	1.768	1.00
61_L	68_L	1.748	1.00
61_L	64_P	1.664	1.00
31_L	55_A	1.622	1.00
49_P	54_T	1.583	1.00
2_G	6_L	1.572	1.00
46_L	70_I	1.553	1.00
40_L	44_F	1.546	1.00
48_I	69_L	1.434	1.00
30_G	58_V	1.434	1.00
55_A	59_G	1.432	1.00
58_V	69_L	1.357	1.00
48_I	73_K	1.344	1.00
33_L	66_V	1.328	1.00
8_L	12_L	1.309	1.00
57_I	69_L	1.276	1.00
33_L	37_V	1.235	1.00
49_P	52_P	1.212	1.00
33_L	63_I	1.178	1.00
41_G	47_H	1.166	1.00
48_I	70_I	1.157	1.00
27_A	55_A	1.151	1.00
11_K	15_K	1.115	1.00
4_L	8_L	1.097	1.00
31_L	50_I	1.094	1.00
16_P	22_K	1.054	1.00
33_L	58_V	1.052	1.00
64_P	67_I	1.051	1.00
50_I	54_T	1.010	1.00
13_L	16_P	0.999	1.00
23_L	27_A	0.984	1.00
41_G	62_G	0.977	1.00
68_L	72_L	0.953	1.00
37_V	41_G	0.936	1.00
11_K	14_L	0.925	1.00
48_I	54_T	0.922	1.00
21_L	24_L	0.916	1.00
9_I	12_L	0.904	1.00
29_L	33_L	0.903	1.00
33_L	36_L	0.894	1.00
5_L	9_I	0.888	1.00
38_N	50_I	0.866	1.00
40_L	43_F	0.857	1.00
68_L	71_L	0.849	1.00
6_L	10_L	0.847	1.00
42_G	45_G	0.845	1.00
10_L	13_L	0.828	1.00
14_L	19_L	0.810	1.00
61_L	65_G	0.796	1.00
63_I	67_I	0.780	1.00
32_V	36_L	0.768	1.00
24_L	67_I	0.766	1.00
8_L	11_K	0.756	0.99
53_I	57_I	0.742	0.99
35_F	50_I	0.742	0.99
26_N	29_L	0.735	0.99
35_F	38_N	0.732	0.99
24_L	27_A	0.724	0.99
38_N	48_I	0.724	0.99
4_L	11_K	0.721	0.99
19_L	22_K	0.716	0.99
41_G	45_G	0.711	0.99
69_L	73_K	0.706	0.99
28_V	32_V	0.688	0.99
34_L	69_L	0.673	0.99
51_N	61_L	0.671	0.99
16_P	20_L	0.665	0.99
34_L	58_V	0.664	0.99
15_K	26_N	0.658	0.99
2_G	9_I	0.649	0.98
25_I	35_F	0.647	0.98
56_L	60_I	0.640	0.98
54_T	65_G	0.640	0.98
34_L	70_I	0.625	0.98
5_L	8_L	0.612	0.98
67_I	74_L	0.611	0.98
6_L	14_L	0.605	0.98
24_L	64_P	0.592	0.97
44_F	74_L	0.584	0.97
7_L	12_L	0.578	0.97
14_L	18_K	0.576	0.97
2_G	10_L	0.573	0.97
28_V	31_L	0.570	0.97
23_L	59_G	0.565	0.96
32_V	60_I	0.561	0.96
49_P	70_I	0.560	0.96
19_L	28_V	0.556	0.96
7_L	10_L	0.552	0.96
52_P	55_A	0.550	0.96
53_I	56_L	0.547	0.96
36_L	39_L	0.533	0.95
17_L	23_L	0.523	0.94
4_L	7_L	0.522	0.94
13_L	17_L	0.522	0.94
30_G	65_G	0.520	0.94
63_I	68_L	0.519	0.94
2_G	7_L	0.517	0.94
51_N	68_L	0.514	0.94
60_I	64_P	0.507	0.93
26_N	62_G	0.506	0.93
65_G	69_L	0.505	0.93
6_L	12_L	0.500	0.93

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
4k0jA	3	0.88	4.9	0.847	Contact Map
5a63B	1	0.6	4.1	0.853	Contact Map
4dx5A	3	0.9067	3.2	0.861	Contact Map
3w9iA	3	0.9067	3.1	0.862	Contact Map
4mt1A	3	0.9733	3	0.862	Contact Map
2kluA	1	0.3867	3	0.863	Contact Map
3ne5A	3	0.9067	2.5	0.868	Contact Map
2jwaA	2	0.2933	2.2	0.872	Contact Map
1ji6A	1	0.4133	1.6	0.882	Contact Map
4dveA	3	0.9733	1.5	0.883	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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