DUF624 - PFAM28P - GREMLIN Contacts

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DUF624 - Protein of unknown function, DUF624

PFAM:	PF04854	Sequences: LIILNLLWLLFTLCSLPVVTIGPATTALYYVTRKWVRGEEEGYIFKDFFKAFKENFKQSTLLGLILLLVGALLYVDL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (72)
Sequences:	6599 (5452)
Seq/√Len:	642.5
META:	0.763

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_W	25_T	4.126	1.00
30_Y	51_A	2.917	1.00
17_P	20_T	2.630	1.00
3_I	45_F	2.139	1.00
8_W	28_L	2.136	1.00
23_P	60_T	1.910	1.00
33_R	37_R	1.836	1.00
14_C	48_F	1.821	1.00
51_A	55_N	1.747	1.00
26_T	59_S	1.733	1.00
15_S	21_I	1.720	1.00
57_K	61_L	1.602	1.00
7_L	45_F	1.532	1.00
32_T	36_V	1.530	1.00
58_Q	61_L	1.526	1.00
60_T	63_G	1.523	1.00
22_G	63_G	1.483	1.00
50_K	54_E	1.478	1.00
4_L	28_L	1.431	1.00
34_K	47_D	1.369	1.00
31_V	47_D	1.337	1.00
51_A	54_E	1.312	1.00
30_Y	34_K	1.241	1.00
72_L	76_D	1.228	1.00
15_S	18_V	1.218	1.00
26_T	55_N	1.218	1.00
14_C	49_F	1.209	1.00
66_L	70_G	1.194	1.00
24_A	52_F	1.186	1.00
34_K	51_A	1.151	1.00
43_Y	46_K	1.148	1.00
45_F	49_F	1.126	1.00
49_F	53_K	1.121	1.00
30_Y	47_D	1.110	1.00
43_Y	47_D	1.066	1.00
13_L	17_P	1.065	1.00
63_G	67_L	1.065	1.00
62_L	66_L	1.062	1.00
56_F	60_T	1.021	1.00
52_F	56_F	1.018	1.00
15_S	20_T	0.964	1.00
32_T	35_W	0.962	1.00
25_T	29_Y	0.953	1.00
29_Y	32_T	0.950	1.00
35_W	41_E	0.919	1.00
16_L	19_V	0.908	1.00
27_A	51_A	0.890	1.00
22_G	59_S	0.889	1.00
27_A	52_F	0.836	1.00
21_I	25_T	0.836	1.00
14_C	17_P	0.829	1.00
71_A	74_Y	0.825	1.00
23_P	52_F	0.821	1.00
58_Q	62_L	0.797	1.00
71_A	75_V	0.794	1.00
36_V	39_E	0.787	1.00
31_V	44_I	0.777	1.00
70_G	74_Y	0.756	1.00
29_Y	33_R	0.754	1.00
34_K	39_E	0.750	1.00
47_D	51_A	0.745	1.00
3_I	7_L	0.740	1.00
7_L	48_F	0.740	1.00
23_P	56_F	0.736	1.00
35_W	38_G	0.736	1.00
14_C	24_A	0.734	1.00
41_E	47_D	0.724	1.00
30_Y	54_E	0.720	1.00
55_N	59_S	0.703	1.00
22_G	60_T	0.696	1.00
27_A	31_V	0.695	1.00
5_N	9_L	0.693	1.00
8_W	29_Y	0.690	1.00
70_G	73_L	0.677	1.00
34_K	42_G	0.676	1.00
49_F	52_F	0.669	1.00
35_W	39_E	0.669	1.00
55_N	58_Q	0.661	1.00
28_L	32_T	0.652	1.00
59_S	63_G	0.627	1.00
57_K	60_T	0.624	1.00
8_W	14_C	0.623	1.00
23_P	27_A	0.611	1.00
19_V	56_F	0.610	1.00
46_K	50_K	0.602	1.00
42_G	47_D	0.595	1.00
46_K	49_F	0.594	1.00
33_R	38_G	0.591	1.00
3_I	6_L	0.586	1.00
67_L	71_A	0.570	1.00
4_L	32_T	0.566	1.00
14_C	23_P	0.564	1.00
25_T	28_L	0.564	1.00
72_L	75_V	0.562	1.00
14_C	52_F	0.559	1.00
24_A	27_A	0.557	1.00
61_L	65_I	0.557	1.00
1_L	35_W	0.548	1.00
33_R	36_V	0.546	1.00
23_P	59_S	0.542	1.00
16_L	20_T	0.541	1.00
38_G	41_E	0.527	0.99
4_L	31_V	0.527	0.99
31_V	42_G	0.526	0.99
15_S	19_V	0.516	0.99
31_V	35_W	0.513	0.99
35_W	47_D	0.509	0.99
8_W	48_F	0.500	0.99

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
3tx3A	2	0.974	6.4	0.859	Contact Map
2zy9A	2	0.8701	5.3	0.864	Contact Map
3hzqA	3	0.3896	5.3	0.864	Contact Map
3j9pD	4	0.987	3.9	0.873	Contact Map
1rh5B	1	0.4286	3.7	0.873	Contact Map
2oarA	7	0.3896	2.7	0.882	Contact Map
4pl0A	2	0.5065	2.6	0.883	Contact Map
4tquM	1	0.4156	2.4	0.885	Contact Map
3j5pB	3	0.9221	2.3	0.887	Contact Map
4wl1A	3	0	2.3	0.887	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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