DUF4260 - PFAM28P - GREMLIN Contacts

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DUF4260 - Domain of unknown function (DUF4260)

PFAM:	PF14079	Sequences: KTLLRLEGLALFAAALALYAQLGGSWWLFALLFLAPDLSMLGYLAGPRVGAITYNLAHTYALPLALAAAGLLLGSPLLLLIGLIWLAHIGFDRALGYGLKYPTGFKDTHLGRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (111)
Sequences:	5712 (4065)
Seq/√Len:	385.8
META:	0.909

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_T	107_D	4.344	1.00
39_S	57_A	3.432	1.00
33_F	91_F	3.300	1.00
11_L	60_Y	3.007	1.00
107_D	112_R	2.681	1.00
24_G	80_L	2.628	1.00
67_A	82_G	2.353	1.00
8_G	90_G	2.249	1.00
15_A	87_A	2.247	1.00
104_G	107_D	2.114	1.00
42_G	53_T	2.004	1.00
12_F	91_F	1.960	1.00
60_Y	86_L	1.949	1.00
52_I	102_P	1.937	1.00
45_A	49_V	1.737	1.00
9_L	94_A	1.647	1.00
70_G	78_L	1.644	1.00
63_P	85_W	1.622	1.00
67_A	79_L	1.545	1.00
29_F	87_A	1.528	1.00
27_W	31_L	1.521	1.00
69_A	73_L	1.509	1.00
60_Y	90_G	1.481	1.00
49_V	53_T	1.479	1.00
8_G	60_Y	1.477	1.00
77_L	81_I	1.460	1.00
16_L	29_F	1.425	1.00
75_S	78_L	1.423	1.00
70_G	82_G	1.387	1.00
15_A	83_L	1.376	1.00
17_A	21_Q	1.372	1.00
2_T	5_R	1.369	1.00
32_L	35_A	1.361	1.00
39_S	53_T	1.330	1.00
40_M	57_A	1.329	1.00
41_L	44_L	1.272	1.00
33_F	87_A	1.245	1.00
11_L	86_L	1.241	1.00
12_F	87_A	1.234	1.00
77_L	80_L	1.199	1.00
25_S	28_L	1.181	1.00
63_P	89_I	1.147	1.00
104_G	112_R	1.147	1.00
15_A	86_L	1.135	1.00
103_T	112_R	1.118	1.00
16_L	20_A	1.117	1.00
106_K	112_R	1.103	1.00
91_F	95_L	1.094	1.00
17_A	20_A	1.091	1.00
56_L	62_L	1.059	1.00
87_A	91_F	1.055	1.00
53_T	57_A	1.052	1.00
46_G	49_V	1.050	1.00
106_K	111_G	1.046	1.00
11_L	90_G	1.036	1.00
62_L	85_W	0.991	1.00
40_M	97_Y	0.991	1.00
6_L	10_A	0.967	1.00
15_A	90_G	0.959	1.00
18_L	22_L	0.959	1.00
43_Y	100_K	0.946	1.00
47_P	104_G	0.944	1.00
52_I	56_L	0.936	1.00
85_W	89_I	0.932	1.00
62_L	65_A	0.924	1.00
26_W	30_A	0.924	1.00
28_L	32_L	0.891	1.00
4_L	8_G	0.883	1.00
63_P	86_L	0.879	1.00
10_A	64_L	0.867	1.00
70_G	79_L	0.864	1.00
5_R	8_G	0.856	1.00
41_L	45_A	0.855	1.00
60_Y	89_I	0.854	1.00
59_T	89_I	0.853	1.00
10_A	61_A	0.849	1.00
63_P	82_G	0.845	1.00
31_L	35_A	0.845	1.00
32_L	81_I	0.840	1.00
6_L	61_A	0.840	1.00
8_G	11_L	0.830	1.00
48_R	52_I	0.824	1.00
32_L	84_I	0.812	1.00
19_Y	84_I	0.811	1.00
91_F	94_A	0.804	1.00
80_L	84_I	0.774	1.00
76_P	79_L	0.769	1.00
27_W	30_A	0.760	1.00
40_M	105_F	0.758	1.00
20_A	23_G	0.758	1.00
28_L	31_L	0.756	1.00
35_A	38_L	0.755	1.00
32_L	80_L	0.753	1.00
4_L	101_Y	0.748	1.00
66_L	85_W	0.736	1.00
12_F	16_L	0.714	1.00
67_A	71_L	0.703	1.00
2_T	6_L	0.702	1.00
66_L	78_L	0.694	0.99
89_I	94_A	0.692	0.99
11_L	15_A	0.691	0.99
43_Y	51_A	0.687	0.99
57_A	85_W	0.683	0.99
60_Y	85_W	0.680	0.99
40_M	44_L	0.677	0.99
22_L	83_L	0.674	0.99
68_A	72_L	0.674	0.99
82_G	86_L	0.669	0.99
13_A	20_A	0.665	0.99
40_M	53_T	0.664	0.99
19_Y	32_L	0.658	0.99
104_G	111_G	0.655	0.99
59_T	63_P	0.651	0.99
18_L	21_Q	0.650	0.99
34_L	91_F	0.650	0.99
62_L	89_I	0.644	0.99
59_T	62_L	0.643	0.99
29_F	84_I	0.642	0.99
62_L	86_L	0.639	0.99
20_A	26_W	0.628	0.99
22_L	79_L	0.627	0.99
14_A	18_L	0.624	0.99
64_L	86_L	0.619	0.99
47_P	51_A	0.617	0.99
19_Y	29_F	0.615	0.99
81_I	85_W	0.608	0.99
35_A	81_I	0.607	0.99
19_Y	26_W	0.592	0.98
47_P	103_T	0.589	0.98
18_L	83_L	0.587	0.98
13_A	17_A	0.585	0.98
101_Y	104_G	0.583	0.98
19_Y	23_G	0.565	0.98
61_A	89_I	0.562	0.98
49_V	52_I	0.560	0.98
38_L	57_A	0.560	0.98
64_L	67_A	0.557	0.98
28_L	80_L	0.557	0.98
65_A	69_A	0.556	0.98
88_H	92_D	0.553	0.97
74_G	77_L	0.551	0.97
6_L	9_L	0.548	0.97
107_D	111_G	0.544	0.97
66_L	82_G	0.543	0.97
101_Y	106_K	0.537	0.97
42_G	49_V	0.535	0.97
48_R	102_P	0.530	0.97
4_L	110_L	0.528	0.97
55_N	105_F	0.526	0.97
73_L	76_P	0.525	0.97
5_R	111_G	0.525	0.97
19_Y	24_G	0.520	0.96
60_Y	64_L	0.520	0.96
46_G	50_G	0.519	0.96
57_A	61_A	0.518	0.96
29_F	32_L	0.518	0.96
16_L	33_F	0.515	0.96
24_G	28_L	0.512	0.96
100_K	105_F	0.508	0.96
47_P	111_G	0.508	0.96
43_Y	47_P	0.507	0.96
16_L	23_G	0.506	0.96
55_N	100_K	0.505	0.96
15_A	29_F	0.502	0.96
38_L	41_L	0.501	0.96
40_M	50_G	0.500	0.95

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
1vhkA	3	0.2212	23.8	0.922	Contact Map
4l69A	2	0.2212	9.8	0.934	Contact Map
3gvaA	1	0.2655	2.7	0.95	Contact Map
4b03D	5	0.3451	2.6	0.95	Contact Map
2gsvA	3	0.1416	2.6	0.95	Contact Map
4dveA	3	0.9735	1.7	0.955	Contact Map
3j27B	2	0.3186	1.3	0.958	Contact Map
4cctD	2	0.3363	1.2	0.959	Contact Map
2wvxA	2	0.5752	1.2	0.959	Contact Map
4cbfB	2	0.3363	1.2	0.959	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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