DUF4279 - PFAM28P - GREMLIN Contacts

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DUF4279 - Domain of unknown function (DUF4279)

PFAM:	PF14106	Sequences: FGDDLDPDEITRLLGLEPTRSWRKGDPRRGGSRVRKTGSWSLSSGLEESEDLEEHLDELLDRLEPKKEALRELKERYGVDIFCGVFLYSSNGGFPGLELSPETLRRLAELGAELDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (114)
Sequences:	5721 (5092)
Seq/√Len:	476.9
META:	0.916

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_W	35_R	2.820	1.00
64_E	106_R	2.587	1.00
105_R	109_E	2.420	1.00
22_W	39_S	2.351	1.00
11_T	40_W	2.257	1.00
6_D	23_R	2.219	1.00
11_T	18_P	2.216	1.00
9_E	12_R	2.088	1.00
66_K	69_A	2.066	1.00
23_R	26_D	2.029	1.00
28_R	35_R	2.028	1.00
67_K	109_E	1.910	1.00
67_K	71_R	1.776	1.00
105_R	108_A	1.757	1.00
44_S	55_H	1.719	1.00
98_E	115_D	1.716	1.00
27_P	34_V	1.715	1.00
104_L	108_A	1.626	1.00
7_P	23_R	1.613	1.00
9_E	13_L	1.569	1.00
98_E	113_E	1.524	1.00
44_S	48_E	1.491	1.00
19_T	42_L	1.478	1.00
20_R	41_S	1.466	1.00
57_D	102_E	1.452	1.00
3_D	24_K	1.405	1.00
10_I	14_L	1.405	1.00
5_L	38_G	1.399	1.00
45_G	58_E	1.359	1.00
101_P	113_E	1.339	1.00
60_L	106_R	1.338	1.00
106_R	110_L	1.328	1.00
72_E	76_R	1.325	1.00
53_E	100_S	1.325	1.00
13_L	72_E	1.317	1.00
28_R	33_R	1.315	1.00
28_R	34_V	1.283	1.00
21_S	38_G	1.280	1.00
61_D	106_R	1.274	1.00
57_D	103_T	1.260	1.00
46_L	55_H	1.199	1.00
8_D	12_R	1.178	1.00
105_R	111_G	1.176	1.00
44_S	47_E	1.174	1.00
50_E	54_E	1.166	1.00
24_K	38_G	1.164	1.00
101_P	108_A	1.160	1.00
64_E	67_K	1.159	1.00
42_L	62_R	1.157	1.00
13_L	69_A	1.150	1.00
100_S	103_T	1.145	1.00
53_E	57_D	1.144	1.00
8_D	23_R	1.134	1.00
53_E	103_T	1.128	1.00
7_P	38_G	1.125	1.00
22_W	37_T	1.124	1.00
47_E	58_E	1.121	1.00
42_L	63_L	1.105	1.00
13_L	76_R	1.090	1.00
55_H	58_E	1.080	1.00
26_D	35_R	1.068	1.00
6_D	9_E	1.020	1.00
2_G	6_D	1.006	1.00
101_P	111_G	0.987	1.00
57_D	106_R	0.987	1.00
49_S	55_H	0.976	1.00
44_S	58_E	0.973	1.00
66_K	70_L	0.971	1.00
57_D	100_S	0.964	1.00
74_K	111_G	0.964	1.00
71_R	74_K	0.961	1.00
58_E	62_R	0.950	1.00
16_L	62_R	0.927	1.00
55_H	59_L	0.924	1.00
89_S	92_G	0.921	1.00
70_L	110_L	0.921	1.00
103_T	106_R	0.907	1.00
99_L	104_L	0.907	1.00
101_P	104_L	0.903	1.00
2_G	38_G	0.896	1.00
107_L	114_L	0.893	1.00
57_D	61_D	0.889	1.00
6_D	38_G	0.873	1.00
22_W	26_D	0.870	1.00
23_R	38_G	0.862	1.00
9_E	76_R	0.861	1.00
68_E	71_R	0.845	1.00
103_T	107_L	0.840	1.00
14_L	66_K	0.835	1.00
33_R	36_K	0.835	1.00
45_G	48_E	0.831	1.00
7_P	11_T	0.817	1.00
7_P	21_S	0.811	1.00
51_D	54_E	0.805	1.00
74_K	79_V	0.792	1.00
27_P	33_R	0.786	1.00
79_V	112_A	0.785	1.00
69_A	72_E	0.785	1.00
4_D	76_R	0.784	1.00
19_T	62_R	0.764	1.00
2_G	77_Y	0.760	1.00
19_T	43_S	0.748	1.00
16_L	42_L	0.748	1.00
29_R	32_S	0.747	1.00
20_R	39_S	0.745	1.00
13_L	73_L	0.744	1.00
8_D	17_E	0.736	1.00
64_E	70_L	0.736	1.00
87_L	93_G	0.728	1.00
19_T	40_W	0.727	1.00
27_P	30_G	0.724	1.00
74_K	81_I	0.721	1.00
35_R	39_S	0.712	1.00
81_I	112_A	0.711	1.00
72_E	75_E	0.703	1.00
8_D	21_S	0.703	1.00
101_P	105_R	0.701	1.00
106_R	109_E	0.700	1.00
90_S	93_G	0.696	1.00
107_L	112_A	0.694	1.00
52_L	85_V	0.684	1.00
71_R	109_E	0.680	1.00
102_E	106_R	0.679	1.00
93_G	96_G	0.678	1.00
64_E	109_E	0.678	1.00
71_R	75_E	0.669	1.00
11_T	21_S	0.667	1.00
99_L	103_T	0.660	1.00
24_K	36_K	0.656	1.00
22_W	28_R	0.649	1.00
56_L	103_T	0.648	1.00
104_L	114_L	0.645	1.00
70_L	81_I	0.620	0.99
94_F	97_L	0.616	0.99
71_R	111_G	0.616	0.99
12_R	15_G	0.614	0.99
86_F	89_S	0.611	0.99
81_I	85_V	0.611	0.99
87_L	92_G	0.608	0.99
20_R	43_S	0.606	0.99
62_R	65_P	0.605	0.99
11_T	14_L	0.593	0.99
60_L	103_T	0.592	0.99
18_P	21_S	0.592	0.99
62_R	66_K	0.591	0.99
45_G	62_R	0.586	0.99
4_D	24_K	0.582	0.99
52_L	83_C	0.580	0.99
56_L	83_C	0.578	0.99
74_K	77_Y	0.574	0.99
68_E	72_E	0.573	0.99
6_D	12_R	0.565	0.99
16_L	66_K	0.561	0.99
11_T	15_G	0.560	0.99
14_L	70_L	0.556	0.99
28_R	31_G	0.552	0.99
102_E	105_R	0.550	0.99
91_N	95_P	0.549	0.99
82_F	115_D	0.547	0.99
54_E	57_D	0.541	0.99
89_S	94_F	0.539	0.99
58_E	61_D	0.535	0.98
15_G	66_K	0.533	0.98
50_E	55_H	0.532	0.98
10_I	40_W	0.531	0.98
87_L	91_N	0.527	0.98
99_L	114_L	0.527	0.98
101_P	114_L	0.523	0.98
50_E	53_E	0.522	0.98
11_T	17_E	0.507	0.98
28_R	32_S	0.500	0.98

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
1avoB	3	0.5776	17.1	0.874	Contact Map
4nqwA	1	0.319	14.1	0.878	Contact Map
4jdpA	2	0.6034	9	0.889	Contact Map
3cuqA	1	0.4052	7.2	0.893	Contact Map
1s7oA	3	0.6724	7.1	0.894	Contact Map
1svdM	3	0.7931	6.9	0.894	Contact Map
1rp3A	1	0.3448	6.1	0.897	Contact Map
4j2oA	5	0.4052	5.8	0.898	Contact Map
4g5hA	3	0.5431	5.8	0.898	Contact Map
3s6jA	2	0.5862	5.5	0.899	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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