bPH_6 - PFAM28P - GREMLIN Contacts

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bPH_6 - Bacterial PH domain

PFAM:	PF10756	Sequences: RPRVVADADGLTVRNLLGTRRLPWAEVVGVRFPRGRRWARLDLADGELVALMAVQLGDGPERAAAALRRLRDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (71)
Sequences:	5487 (3378)
Seq/√Len:	400.8
META:	0.737

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_T	21_R	4.414	1.00
23_P	26_E	3.575	1.00
10_G	21_R	2.629	1.00
12_T	19_T	2.499	1.00
5_V	12_T	2.218	1.00
66_A	69_R	2.081	1.00
7_D	21_R	2.000	1.00
7_D	12_T	1.996	1.00
10_G	24_W	1.990	1.00
4_V	51_L	1.926	1.00
14_R	19_T	1.923	1.00
28_V	44_A	1.597	1.00
26_E	44_A	1.596	1.00
9_D	23_P	1.519	1.00
31_R	48_L	1.485	1.00
40_R	48_L	1.444	1.00
9_D	21_R	1.415	1.00
62_R	66_A	1.380	1.00
6_A	24_W	1.368	1.00
7_D	10_G	1.354	1.00
15_N	20_R	1.354	1.00
22_L	49_V	1.354	1.00
61_E	65_A	1.300	1.00
60_P	64_A	1.288	1.00
68_R	71_R	1.265	1.00
6_A	70_L	1.253	1.00
32_F	39_A	1.233	1.00
3_R	14_R	1.183	1.00
28_V	46_G	1.145	1.00
40_R	44_A	1.105	1.00
63_A	67_L	1.065	1.00
11_L	27_V	1.031	1.00
67_L	71_R	1.019	1.00
33_P	40_R	0.997	1.00
14_R	17_L	0.960	1.00
40_R	43_L	0.950	1.00
2_P	15_N	0.931	1.00
16_L	50_A	0.921	1.00
62_R	65_A	0.900	1.00
43_L	47_E	0.885	1.00
65_A	69_R	0.885	1.00
41_L	51_L	0.882	1.00
55_Q	58_D	0.871	1.00
46_G	49_V	0.860	1.00
16_L	52_M	0.857	1.00
54_V	59_G	0.834	1.00
42_D	48_L	0.826	1.00
1_R	18_G	0.822	1.00
61_E	64_A	0.821	1.00
30_V	41_L	0.819	1.00
32_F	56_L	0.815	1.00
41_L	44_A	0.810	1.00
27_V	30_V	0.809	1.00
16_L	35_G	0.803	1.00
59_G	62_R	0.800	1.00
39_A	42_D	0.793	1.00
58_D	63_A	0.772	1.00
58_D	62_R	0.761	1.00
62_R	67_L	0.755	1.00
62_R	68_R	0.751	1.00
2_P	17_L	0.745	1.00
31_R	42_D	0.727	1.00
21_R	24_W	0.682	0.99
32_F	38_W	0.679	0.99
30_V	67_L	0.671	0.99
52_M	55_Q	0.668	0.99
66_A	70_L	0.666	0.99
12_T	68_R	0.666	0.99
13_V	20_R	0.657	0.99
63_A	70_L	0.653	0.99
53_A	60_P	0.644	0.99
2_P	36_R	0.633	0.99
43_L	46_G	0.629	0.99
33_P	38_W	0.626	0.99
27_V	43_L	0.616	0.99
14_R	35_G	0.609	0.99
62_R	71_R	0.599	0.99
29_G	42_D	0.598	0.99
36_R	40_R	0.591	0.99
40_R	50_A	0.587	0.98
65_A	68_R	0.580	0.98
41_L	45_D	0.579	0.98
13_V	32_F	0.578	0.98
22_L	43_L	0.578	0.98
39_A	54_V	0.576	0.98
15_N	37_R	0.573	0.98
54_V	66_A	0.562	0.98
48_L	57_G	0.561	0.98
25_A	28_V	0.561	0.98
51_L	55_Q	0.556	0.98
32_F	55_Q	0.555	0.98
38_W	52_M	0.554	0.98
4_V	41_L	0.551	0.98
67_L	70_L	0.548	0.98
2_P	16_L	0.542	0.97
28_V	42_D	0.541	0.97
13_V	51_L	0.533	0.97
40_R	45_D	0.533	0.97
56_L	60_P	0.529	0.97
9_D	24_W	0.523	0.97
64_A	68_R	0.521	0.97
63_A	66_A	0.520	0.97
47_E	54_V	0.507	0.96
5_V	14_R	0.502	0.96
48_L	51_L	0.501	0.96
58_D	61_E	0.500	0.96

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
2i1jA	3	0.9589	10.6	0.824	Contact Map
4khbD	1	0.9726	8.4	0.831	Contact Map
3f5rA	2	0.9863	7.9	0.833	Contact Map
4yl8A	1	0.9041	6.9	0.838	Contact Map
1h4rA	2	0.9589	6.2	0.841	Contact Map
3pvlA	1	1	4	0.855	Contact Map
4ekuA	2	1	3.1	0.862	Contact Map
4f7gA	1	0.863	2.8	0.865	Contact Map
4tyzA	1	0.9589	2.5	0.87	Contact Map
1hymB	1	0.2603	2.4	0.871	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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