DUF1206 - PFAM28P - GREMLIN Contacts

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DUF1206 - Domain of Unknown Function (DUF1206)

PFAM:	PF06724	Sequences: AGYAARGVVYALIGVLALRAALGSGGSSAGGLDGALATLAGQPFGRWLLGLVALGLIAYGLWQLVEARYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (69)
Sequences:	34802 (22320)
Seq/√Len:	2686.9
META:	0.902

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_L	22_L	2.508	1.00
65_V	69_Y	2.425	1.00
55_G	59_Y	2.305	1.00
15_V	19_R	2.276	1.00
63_Q	66_E	2.241	1.00
19_R	23_G	2.095	1.00
38_T	42_Q	1.972	1.00
47_W	50_G	1.905	1.00
6_R	10_Y	1.703	1.00
38_T	41_G	1.587	1.00
40_A	49_L	1.575	1.00
46_R	50_G	1.546	1.00
62_W	65_V	1.530	1.00
14_G	18_L	1.485	1.00
61_L	65_V	1.479	1.00
9_V	12_L	1.444	1.00
36_L	49_L	1.417	1.00
58_A	62_W	1.401	1.00
19_R	22_L	1.363	1.00
35_A	38_T	1.304	1.00
3_Y	6_R	1.278	1.00
1_A	58_A	1.270	1.00
40_A	46_R	1.264	1.00
30_G	34_G	1.260	1.00
14_G	21_A	1.201	1.00
37_A	41_G	1.180	1.00
30_G	38_T	1.173	1.00
62_W	66_E	1.132	1.00
19_R	24_S	1.126	1.00
64_L	68_R	1.114	1.00
44_F	47_W	1.102	1.00
59_Y	63_Q	1.095	1.00
42_Q	48_L	1.095	1.00
39_L	42_Q	1.085	1.00
18_L	21_A	1.084	1.00
53_A	57_I	1.075	1.00
47_W	51_L	1.074	1.00
11_A	15_V	1.025	1.00
52_V	55_G	1.015	1.00
42_Q	46_R	1.013	1.00
34_G	38_T	1.005	1.00
54_L	58_A	1.002	1.00
5_A	55_G	1.000	1.00
32_L	36_L	0.983	1.00
66_E	69_Y	0.976	1.00
4_A	8_V	0.963	1.00
44_F	48_L	0.938	1.00
33_D	37_A	0.928	1.00
12_L	15_V	0.923	1.00
62_W	68_R	0.905	1.00
50_G	54_L	0.898	1.00
8_V	12_L	0.876	1.00
43_P	46_R	0.855	1.00
33_D	40_A	0.833	1.00
64_L	67_A	0.823	1.00
27_S	30_G	0.822	1.00
12_L	16_L	0.807	1.00
37_A	40_A	0.792	1.00
25_G	28_S	0.792	1.00
6_R	9_V	0.777	1.00
36_L	40_A	0.775	1.00
45_G	49_L	0.767	1.00
17_A	20_A	0.766	1.00
23_G	28_S	0.766	1.00
57_I	61_L	0.752	1.00
40_A	43_P	0.745	1.00
14_G	17_A	0.734	1.00
50_G	53_A	0.730	1.00
6_R	14_G	0.729	1.00
6_R	59_Y	0.713	1.00
20_A	29_A	0.712	1.00
60_G	64_L	0.707	1.00
4_A	7_G	0.700	1.00
61_L	64_L	0.694	1.00
49_L	53_A	0.680	1.00
35_A	39_L	0.677	1.00
10_Y	17_A	0.672	1.00
5_A	52_V	0.668	1.00
25_G	29_A	0.659	1.00
1_A	4_A	0.659	1.00
24_S	28_S	0.622	1.00
52_V	56_L	0.621	1.00
13_I	17_A	0.620	1.00
39_L	45_G	0.612	1.00
6_R	66_E	0.608	1.00
63_Q	69_Y	0.601	1.00
9_V	59_Y	0.599	1.00
60_G	67_A	0.599	1.00
48_L	51_L	0.593	1.00
24_S	27_S	0.584	1.00
12_L	39_L	0.582	1.00
65_V	68_R	0.579	1.00
59_Y	62_W	0.567	1.00
16_L	20_A	0.565	1.00
31_G	35_A	0.558	1.00
13_I	35_A	0.546	1.00
34_G	37_A	0.534	1.00
9_V	16_L	0.533	1.00
6_R	56_L	0.519	1.00
9_V	32_L	0.516	1.00
53_A	56_L	0.511	1.00
10_Y	13_I	0.508	1.00
30_G	33_D	0.503	1.00
51_L	55_G	0.500	1.00

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
4a01A	2	1	7.1	0.821	Contact Map
4wgvA	2	1	6.5	0.824	Contact Map
3j1zP	8	0.8143	6.2	0.826	Contact Map
3h90A	3	0.8143	5.6	0.83	Contact Map
4us3A	1	1	4.7	0.836	Contact Map
3l1lA	2	0.9571	4.3	0.84	Contact Map
2jafA	3	0.4714	3.3	0.848	Contact Map
4av3A	2	1	3.1	0.85	Contact Map
4djkA	2	1	2.4	0.858	Contact Map
3giaA	1	0.9714	2.3	0.861	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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