DUF4280 - PFAM28P - GREMLIN Contacts

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DUF4280 - Domain of unknown function (DUF4280)

PFAM:	PF14107	Sequences: VVMGAMLQCSFGTAPSSLLVLPSNHRVYIGGKPAATIMDNKPMVNIPPFGMCKSPANPTVAAATCIPVTPAPWVPGSPTVLIGGMPALTNTSKLMCAWGGVISITDPGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	109 (109)
Sequences:	4450 (3363)
Seq/√Len:	322.1
META:	0.843

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_M	85_M	2.900	1.00
7_L	104_I	2.832	1.00
77_S	89_T	2.428	1.00
37_I	76_G	2.301	1.00
41_K	44_V	2.165	1.00
3_M	32_K	2.119	1.00
8_Q	105_T	2.083	1.00
70_P	97_A	2.037	1.00
93_K	103_S	2.015	1.00
13_T	51_M	1.991	1.00
16_S	48_P	1.892	1.00
6_M	106_D	1.871	1.00
31_G	84_G	1.794	1.00
13_T	53_K	1.784	1.00
40_N	70_P	1.735	1.00
60_V	63_A	1.729	1.00
89_T	92_S	1.724	1.00
37_I	86_P	1.722	1.00
43_M	47_P	1.710	1.00
74_V	95_M	1.692	1.00
11_F	53_K	1.679	1.00
24_N	83_G	1.664	1.00
6_M	17_S	1.653	1.00
3_M	19_L	1.593	1.00
8_Q	103_S	1.571	1.00
40_N	69_T	1.545	1.00
69_T	94_L	1.501	1.00
82_I	87_A	1.491	1.00
28_Y	33_P	1.472	1.00
5_A	108_G	1.398	1.00
93_K	101_V	1.390	1.00
59_T	66_I	1.375	1.00
10_S	103_S	1.355	1.00
57_N	60_V	1.337	1.00
95_M	101_V	1.323	1.00
36_T	85_M	1.310	1.00
90_N	107_P	1.298	1.00
43_M	66_I	1.297	1.00
29_I	34_A	1.291	1.00
19_L	47_P	1.285	1.00
11_F	54_S	1.279	1.00
68_V	97_A	1.248	1.00
40_N	72_P	1.234	1.00
16_S	47_P	1.203	1.00
2_V	29_I	1.182	1.00
28_Y	81_L	1.173	1.00
3_M	20_V	1.169	1.00
37_I	72_P	1.156	1.00
55_P	61_A	1.142	1.00
21_L	24_N	1.113	1.00
34_A	82_I	1.091	1.00
34_A	87_A	1.079	1.00
35_A	88_L	1.074	1.00
23_S	26_R	1.057	1.00
69_T	102_I	1.055	1.00
81_L	86_P	1.055	1.00
75_P	92_S	1.054	1.00
6_M	15_P	1.053	1.00
61_A	64_T	1.053	1.00
7_L	47_P	1.050	1.00
76_G	88_L	1.043	1.00
75_P	91_T	1.032	1.00
26_R	83_G	1.005	1.00
66_I	98_W	0.989	1.00
10_S	100_G	0.986	1.00
3_M	33_P	0.966	1.00
51_M	60_V	0.957	1.00
13_T	50_G	0.952	1.00
54_S	61_A	0.949	1.00
30_G	109_Q	0.948	1.00
29_I	32_K	0.932	1.00
88_L	104_I	0.928	1.00
7_L	35_A	0.922	1.00
38_M	72_P	0.919	1.00
76_G	92_S	0.918	1.00
14_A	50_G	0.915	1.00
24_N	33_P	0.902	1.00
56_A	99_G	0.887	1.00
54_S	99_G	0.886	1.00
74_V	93_K	0.875	1.00
21_L	35_A	0.853	1.00
19_L	35_A	0.846	1.00
8_Q	53_K	0.844	1.00
54_S	57_N	0.820	1.00
36_T	39_D	0.806	1.00
71_A	97_A	0.802	1.00
59_T	63_A	0.801	1.00
1_V	104_I	0.800	1.00
31_G	34_A	0.797	1.00
46_I	69_T	0.789	1.00
76_G	86_P	0.785	1.00
24_N	27_V	0.757	0.99
2_V	32_K	0.756	0.99
77_S	92_S	0.752	0.99
7_L	46_I	0.751	0.99
59_T	62_A	0.748	0.99
11_F	101_V	0.731	0.99
27_V	82_I	0.708	0.99
46_I	67_P	0.707	0.99
56_A	61_A	0.700	0.99
2_V	30_G	0.696	0.99
55_P	62_A	0.695	0.99
18_L	35_A	0.695	0.99
28_Y	32_K	0.678	0.99
68_V	98_W	0.673	0.99
67_P	97_A	0.670	0.99
4_G	32_K	0.669	0.99
18_L	21_L	0.668	0.99
55_P	64_T	0.665	0.99
54_S	58_P	0.651	0.98
58_P	61_A	0.650	0.98
2_V	108_G	0.649	0.98
77_S	87_A	0.641	0.98
75_P	93_K	0.640	0.98
51_M	57_N	0.640	0.98
23_S	41_K	0.633	0.98
2_V	5_A	0.631	0.98
28_Y	31_G	0.630	0.98
60_V	64_T	0.626	0.98
23_S	44_V	0.624	0.98
21_L	44_V	0.618	0.98
12_G	49_F	0.612	0.98
104_I	107_P	0.604	0.97
6_M	105_T	0.604	0.97
43_M	59_T	0.601	0.97
81_L	84_G	0.601	0.97
14_A	51_M	0.600	0.97
40_N	71_A	0.598	0.97
1_V	5_A	0.587	0.97
74_V	86_P	0.586	0.97
7_L	16_S	0.581	0.97
90_N	106_D	0.579	0.97
57_N	98_W	0.579	0.97
54_S	98_W	0.577	0.97
43_M	48_P	0.576	0.97
69_T	97_A	0.573	0.96
21_L	33_P	0.571	0.96
11_F	55_P	0.568	0.96
51_M	59_T	0.566	0.96
20_V	23_S	0.566	0.96
91_T	103_S	0.563	0.96
80_V	87_A	0.561	0.96
81_L	85_M	0.560	0.96
77_S	80_V	0.552	0.96
57_N	64_T	0.551	0.96
7_L	49_F	0.546	0.95
88_L	94_L	0.546	0.95
18_L	22_P	0.546	0.95
41_K	68_V	0.545	0.95
57_N	61_A	0.545	0.95
43_M	46_I	0.542	0.95
30_G	34_A	0.538	0.95
55_P	58_P	0.532	0.95
74_V	78_P	0.531	0.95
36_T	88_L	0.526	0.94
5_A	106_D	0.523	0.94
3_M	35_A	0.523	0.94
80_V	90_N	0.515	0.94
8_Q	15_P	0.515	0.94
49_F	102_I	0.514	0.94
19_L	23_S	0.511	0.93
21_L	26_R	0.511	0.93
41_K	47_P	0.501	0.93
12_G	16_S	0.500	0.93

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
4jiwD	1	0.789	11.3	0.896	Contact Map
4jivD	1	0.789	9.1	0.9	Contact Map
4ku0D	1	0.7982	7	0.905	Contact Map
3maeA	3	0.2569	1.7	0.931	Contact Map
4rkuN	1	0.5596	1.7	0.931	Contact Map
2nmmA	3	0.7339	1.5	0.932	Contact Map
2g7bA	1	0.3945	1.4	0.934	Contact Map
4oh4F	1	0.0826	1.2	0.937	Contact Map
1kdgA	4	0.3394	1.1	0.938	Contact Map
2wscN	1	0.5596	1	0.939	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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