DUF4870 - PFAM28P - GREMLIN Contacts

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DUF4870 - Domain of unknown function (DUF4870)

PFAM:	PF09685	Sequences: DERTWAMLAHLSGLAGLLIPFGGFIGPLIIWLIKKDKSPFVRFHAKQALNFQISLLIYGIVLGILGFIPLIGFLLLLLLLLLLGLAALVLWIIAAIKAYQGERYRYPLIGRFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (104)
Sequences:	26185 (19380)
Seq/√Len:	1900.3
META:	0.91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_K	102_E	3.656	1.00
34_K	37_K	3.193	1.00
43_F	103_R	2.447	1.00
42_R	46_K	2.410	1.00
55_L	87_A	2.321	1.00
86_A	90_L	2.261	1.00
97_K	100_Q	2.152	1.00
54_S	58_Y	2.128	1.00
6_A	40_F	2.125	1.00
78_L	81_L	2.101	1.00
105_R	111_R	2.088	1.00
89_V	93_I	1.964	1.00
93_I	97_K	1.824	1.00
87_A	91_W	1.788	1.00
7_M	99_Y	1.759	1.00
11_L	95_A	1.674	1.00
92_I	96_I	1.672	1.00
12_S	26_G	1.591	1.00
47_Q	111_R	1.569	1.00
94_A	104_Y	1.549	1.00
91_W	95_A	1.522	1.00
29_I	33_I	1.470	1.00
46_K	50_N	1.437	1.00
31_W	42_R	1.398	1.00
9_A	45_A	1.362	1.00
44_H	103_R	1.357	1.00
42_R	45_A	1.343	1.00
7_M	11_L	1.326	1.00
94_A	106_Y	1.316	1.00
5_W	30_I	1.310	1.00
10_H	106_Y	1.303	1.00
28_L	32_L	1.272	1.00
38_S	41_V	1.262	1.00
62_L	79_L	1.229	1.00
26_G	30_I	1.195	1.00
13_G	91_W	1.191	1.00
4_T	8_L	1.167	1.00
60_I	64_I	1.161	1.00
23_G	56_L	1.135	1.00
9_A	48_A	1.135	1.00
67_F	70_L	1.129	1.00
51_F	55_L	1.129	1.00
97_K	104_Y	1.099	1.00
81_L	85_L	1.093	1.00
39_P	103_R	1.067	1.00
40_F	44_H	1.053	1.00
93_I	96_I	1.051	1.00
43_F	47_Q	1.033	1.00
59_G	62_L	1.028	1.00
51_F	106_Y	1.024	1.00
9_A	41_V	1.021	1.00
84_G	88_L	1.005	1.00
20_P	23_G	1.005	1.00
5_W	34_K	0.991	1.00
95_A	99_Y	0.984	1.00
65_L	69_P	0.978	1.00
40_F	43_F	0.972	1.00
54_S	109_I	0.970	1.00
50_N	110_G	0.966	1.00
51_F	90_L	0.953	1.00
7_M	95_A	0.946	1.00
81_L	84_G	0.942	1.00
13_G	52_Q	0.937	1.00
96_I	99_Y	0.932	1.00
4_T	99_Y	0.926	1.00
43_F	105_R	0.912	1.00
9_A	30_I	0.905	1.00
105_R	110_G	0.903	1.00
47_Q	109_I	0.896	1.00
35_K	42_R	0.889	1.00
50_N	53_I	0.888	1.00
31_W	46_K	0.884	1.00
59_G	63_G	0.884	1.00
50_N	54_S	0.884	1.00
47_Q	105_R	0.877	1.00
96_I	100_Q	0.877	1.00
8_L	12_S	0.869	1.00
40_F	103_R	0.867	1.00
48_A	52_Q	0.842	1.00
24_F	27_P	0.839	1.00
22_G	26_G	0.831	1.00
69_P	72_G	0.821	1.00
31_W	35_K	0.817	1.00
50_N	112_F	0.817	1.00
93_I	104_Y	0.816	1.00
98_A	103_R	0.815	1.00
59_G	80_L	0.812	1.00
69_P	73_F	0.807	1.00
62_L	65_L	0.801	1.00
60_I	63_G	0.800	1.00
27_P	30_I	0.785	1.00
52_Q	87_A	0.768	1.00
61_V	64_I	0.760	1.00
48_A	94_A	0.759	1.00
25_I	29_I	0.744	1.00
90_L	94_A	0.743	1.00
31_W	45_A	0.730	1.00
83_L	87_A	0.708	1.00
18_L	22_G	0.708	1.00
47_Q	110_G	0.705	1.00
10_H	44_H	0.704	1.00
4_T	7_M	0.702	1.00
52_Q	55_L	0.699	1.00
70_L	73_F	0.698	1.00
44_H	47_Q	0.693	1.00
54_S	110_G	0.693	1.00
51_F	94_A	0.689	1.00
85_L	89_V	0.689	1.00
53_I	56_L	0.689	1.00
52_Q	91_W	0.689	1.00
66_G	69_P	0.686	1.00
78_L	82_L	0.680	1.00
51_F	87_A	0.678	1.00
13_G	48_A	0.676	1.00
31_W	34_K	0.666	1.00
39_P	46_K	0.643	1.00
31_W	49_L	0.641	1.00
59_G	84_G	0.638	1.00
90_L	93_I	0.635	1.00
34_K	38_S	0.634	1.00
44_H	98_A	0.625	1.00
84_G	87_A	0.622	1.00
19_I	22_G	0.617	1.00
27_P	31_W	0.613	1.00
5_W	9_A	0.609	1.00
30_I	45_A	0.608	1.00
59_G	65_L	0.604	1.00
24_F	28_L	0.603	1.00
63_G	67_F	0.598	1.00
61_V	65_L	0.589	1.00
51_F	109_I	0.585	1.00
32_L	36_D	0.579	1.00
3_R	40_F	0.577	1.00
58_Y	83_L	0.575	1.00
6_A	9_A	0.573	1.00
30_I	34_K	0.573	1.00
28_L	31_W	0.572	1.00
80_L	84_G	0.572	1.00
27_P	49_L	0.571	1.00
67_F	71_I	0.561	1.00
49_L	53_I	0.557	1.00
109_I	112_F	0.555	1.00
64_I	68_I	0.554	1.00
66_G	70_L	0.554	1.00
85_L	88_L	0.551	1.00
6_A	44_H	0.547	1.00
10_H	13_G	0.539	1.00
82_L	86_A	0.533	1.00
63_G	68_I	0.526	1.00
43_F	46_K	0.524	1.00
50_N	109_I	0.521	1.00
90_L	106_Y	0.519	1.00
19_I	23_G	0.507	1.00
73_F	77_L	0.504	1.00
41_V	45_A	0.503	1.00
65_L	68_I	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
4bwzA	2	0.3274	7.9	0.888	Contact Map
4httA	1	0.885	4	0.903	Contact Map
2a9hA	4	0.292	3.1	0.907	Contact Map
2x2zA	1	0.0354	3	0.908	Contact Map
4bw5A	2	0.2832	2.1	0.916	Contact Map
3mktA	1	1	1.8	0.919	Contact Map
4d6uD	1	0.3805	1.7	0.92	Contact Map
4humA	1	0.9912	1.6	0.921	Contact Map
1pp9D	2	0.3805	1.6	0.921	Contact Map
2mfrA	1	0.3982	1.6	0.921	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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