DUF4907 - PFAM28P - GREMLIN Contacts

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DUF4907 - Domain of unknown function (DUF4907)

PFAM:	PF16250	Sequences: ETFKTNNGWGYDILVNGKLYIHQPSIPAIPGNKGFKTKEDAEKVAELVIEKIKKGEPPTVTIEELDS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (63)
Sequences:	2077 (1573)
Seq/√Len:	198.1
META:	0.946

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_D	22_H	5.029	1.00
14_L	19_L	2.576	1.00
63_E	66_D	2.397	1.00
11_Y	48_V	2.270	1.00
51_K	64_E	2.128	1.00
36_K	40_D	2.024	1.00
37_T	40_D	2.020	1.00
15_V	20_Y	2.010	1.00
42_E	46_E	1.986	1.00
28_A	62_I	1.748	1.00
60_V	65_L	1.724	1.00
35_F	44_V	1.659	1.00
38_K	42_E	1.636	1.00
44_V	60_V	1.601	1.00
25_S	32_N	1.589	1.00
4_K	8_G	1.442	1.00
62_I	66_D	1.426	1.00
26_I	35_F	1.399	1.00
12_D	19_L	1.356	1.00
50_E	54_K	1.297	1.00
5_T	34_G	1.295	1.00
40_D	44_V	1.273	1.00
49_I	53_K	1.267	1.00
40_D	43_K	1.230	1.00
48_V	60_V	1.172	1.00
47_L	60_V	1.131	1.00
28_A	65_L	1.061	1.00
45_A	49_I	1.052	1.00
9_W	45_A	1.028	1.00
20_Y	52_I	1.016	1.00
13_I	49_I	0.974	0.99
51_K	58_P	0.946	0.99
8_G	34_G	0.944	0.99
43_K	47_L	0.882	0.99
49_I	52_I	0.865	0.99
62_I	65_L	0.854	0.99
26_I	29_I	0.845	0.99
9_W	38_K	0.830	0.98
8_G	29_I	0.808	0.98
12_D	24_P	0.800	0.98
13_I	48_V	0.798	0.98
7_N	34_G	0.792	0.98
21_I	52_I	0.791	0.98
33_K	36_K	0.784	0.98
15_V	53_K	0.783	0.98
5_T	9_W	0.776	0.97
4_K	7_N	0.776	0.97
19_L	22_H	0.755	0.97
14_L	22_H	0.744	0.97
50_E	53_K	0.741	0.97
47_L	66_D	0.732	0.96
27_P	48_V	0.720	0.96
29_I	33_K	0.703	0.95
14_L	17_G	0.695	0.95
11_Y	23_Q	0.684	0.95
5_T	8_G	0.683	0.95
30_P	34_G	0.680	0.95
9_W	35_F	0.680	0.95
39_E	43_K	0.676	0.94
15_V	52_I	0.673	0.94
47_L	51_K	0.667	0.94
47_L	50_E	0.664	0.94
52_I	55_G	0.658	0.94
7_N	30_P	0.657	0.93
4_K	9_W	0.653	0.93
26_I	31_G	0.651	0.93
24_P	56_E	0.640	0.93
7_N	32_N	0.634	0.92
30_P	62_I	0.633	0.92
25_S	31_G	0.621	0.91
41_A	52_I	0.611	0.91
9_W	36_K	0.607	0.90
9_W	58_P	0.601	0.90
11_Y	28_A	0.598	0.90
42_E	49_I	0.588	0.89
28_A	60_V	0.585	0.89
50_E	63_E	0.583	0.89
4_K	38_K	0.575	0.88
6_N	32_N	0.568	0.87
17_G	46_E	0.560	0.87
30_P	33_K	0.557	0.86
16_N	30_P	0.557	0.86
56_E	66_D	0.550	0.86
46_E	53_K	0.550	0.86
44_V	47_L	0.543	0.85
51_K	57_P	0.529	0.83
13_I	61_T	0.526	0.83
46_E	50_E	0.524	0.83
52_I	56_E	0.518	0.82
10_G	34_G	0.512	0.81
9_W	20_Y	0.511	0.81
23_Q	64_E	0.510	0.81
31_G	62_I	0.501	0.80
55_G	66_D	0.500	0.80

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
3d3yA	1	0.8657	15.9	0.879	Contact Map
4l3tA	1	0.7164	14.9	0.88	Contact Map
3syxA	1	0.8209	12.8	0.884	Contact Map
1hr6B	1	0.9552	11.5	0.886	Contact Map
3amjB	1	0.8955	10.6	0.888	Contact Map
1gz6A	2	0.8507	10.1	0.889	Contact Map
1pp9B	2	0.8955	10.1	0.889	Contact Map
3ih6A	5	0.8657	9.6	0.89	Contact Map
3gwbA	2	0.8955	9	0.891	Contact Map
3amiA	2	0.9254	8.9	0.891	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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