bPH_4 - PFAM28P - GREMLIN Contacts

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bPH_4 - Bacterial PH domain

PFAM:	PF06713	Sequences: TRYTITDDELIIRSGPFRWRIPISDITSIEPTRNPLSSPALSLDRLEIRYGKGDSILISPKDKEEFIEELKKRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (73)
Sequences:	3975 (3269)
Seq/√Len:	382.6
META:	0.866

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_D	65_E	4.129	1.00
5_I	23_I	2.546	1.00
28_S	49_R	2.532	1.00
9_E	20_R	2.340	1.00
69_E	72_K	2.148	1.00
31_P	63_K	2.141	1.00
30_E	47_E	2.140	1.00
23_I	73_R	2.072	1.00
44_D	63_K	1.993	1.00
27_T	51_G	1.922	1.00
22_P	25_D	1.886	1.00
12_I	56_I	1.666	1.00
32_T	57_L	1.647	1.00
38_S	45_R	1.519	1.00
45_R	57_L	1.506	1.00
34_N	57_L	1.504	1.00
47_E	55_S	1.423	1.00
69_E	73_R	1.393	1.00
33_R	44_D	1.391	1.00
25_D	51_G	1.344	1.00
50_Y	56_I	1.338	1.00
30_E	49_R	1.326	1.00
11_I	20_R	1.284	1.00
5_I	69_E	1.241	1.00
9_E	23_I	1.235	1.00
2_R	13_R	1.226	1.00
29_I	70_L	1.201	1.00
26_I	48_I	1.166	1.00
31_P	46_L	1.118	1.00
6_T	11_I	1.116	1.00
64_E	68_E	1.078	1.00
51_G	54_D	1.068	1.00
68_E	71_K	1.034	1.00
4_T	11_I	1.022	1.00
65_E	68_E	1.010	1.00
29_I	46_L	1.004	1.00
9_E	22_P	1.001	1.00
27_T	49_R	0.988	1.00
21_I	50_Y	0.987	1.00
8_D	24_S	0.985	1.00
65_E	69_E	0.981	1.00
46_L	58_I	0.959	1.00
40_A	59_S	0.933	1.00
29_I	67_I	0.915	1.00
1_T	41_L	0.912	1.00
32_T	43_L	0.897	1.00
42_S	45_R	0.896	1.00
7_D	23_I	0.878	1.00
13_R	18_R	0.875	1.00
37_S	45_R	0.875	1.00
11_I	18_R	0.868	1.00
6_T	9_E	0.864	1.00
42_S	59_S	0.862	1.00
19_W	56_I	0.850	1.00
40_A	45_R	0.845	1.00
34_N	37_S	0.829	1.00
14_S	19_W	0.807	1.00
10_L	48_I	0.797	1.00
4_T	13_R	0.782	1.00
32_T	36_L	0.756	1.00
12_I	39_P	0.755	1.00
35_P	43_L	0.744	1.00
68_E	72_K	0.742	1.00
49_R	55_S	0.741	1.00
47_E	57_L	0.734	1.00
31_P	64_E	0.727	1.00
48_I	58_I	0.724	1.00
12_I	19_W	0.719	1.00
6_T	23_I	0.712	1.00
26_I	70_L	0.711	1.00
46_L	67_I	0.704	1.00
31_P	67_I	0.703	1.00
1_T	14_S	0.699	0.99
32_T	35_P	0.688	0.99
67_I	71_K	0.672	0.99
39_P	45_R	0.672	0.99
52_K	55_S	0.668	0.99
38_S	57_L	0.653	0.99
27_T	54_D	0.641	0.99
8_D	22_P	0.638	0.99
50_Y	54_D	0.627	0.99
36_L	57_L	0.625	0.99
34_N	38_S	0.618	0.99
59_S	66_F	0.618	0.99
32_T	47_E	0.616	0.99
32_T	38_S	0.608	0.99
8_D	73_R	0.608	0.99
21_I	56_I	0.606	0.99
42_S	58_I	0.593	0.98
60_P	66_F	0.587	0.98
5_I	73_R	0.586	0.98
32_T	45_R	0.585	0.98
62_D	69_E	0.573	0.98
38_S	41_L	0.568	0.98
63_K	67_I	0.566	0.98
5_I	29_I	0.560	0.98
12_I	21_I	0.554	0.97
6_T	20_R	0.542	0.97
19_W	39_P	0.539	0.97
8_D	23_I	0.537	0.97
38_S	43_L	0.537	0.97
43_L	57_L	0.536	0.97
23_I	26_I	0.535	0.97
10_L	58_I	0.531	0.97
41_L	59_S	0.518	0.96
2_R	6_T	0.515	0.96
25_D	54_D	0.507	0.96
37_S	57_L	0.505	0.96
2_R	11_I	0.502	0.95
21_I	26_I	0.500	0.95

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
4chmA	1	1	32.7	0.815	Contact Map
4chjA	1	0.9189	29.3	0.819	Contact Map
4r8gE	1	0.7838	26.4	0.824	Contact Map
4tyzA	1	0.9324	26	0.824	Contact Map
3a98B	1	1	19.6	0.834	Contact Map
1icwA	2	0.8514	18.8	0.835	Contact Map
1cq3A	2	0.8649	16.8	0.839	Contact Map
4y93A	1	1	13.2	0.846	Contact Map
1maiA	1	1	12.8	0.847	Contact Map
2w42A	1	0.7838	12.7	0.848	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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