DUF1622 - PFAM28P - GREMLIN Contacts

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DUF1622 - Protein of unknown function (DUF1622)

PFAM:	PF07784	Sequences: GALVALVRFLRRLLRRRRGDAYRRLRLRLGRALLLGLEFLVAADIIRTVAVPTLESVGVLGAIVLIRTFLSFFLEVEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	78 (77)
Sequences:	10364 (6374)
Seq/√Len:	726.4
META:	0.936

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_L	25_L	4.331	1.00
54_L	58_G	4.319	1.00
2_A	29_L	2.475	1.00
11_R	15_R	2.327	1.00
72_F	75_E	2.285	1.00
8_R	11_R	2.203	1.00
55_E	59_V	1.805	1.00
57_V	62_A	1.786	1.00
41_V	64_V	1.757	1.00
72_F	76_V	1.755	1.00
73_F	76_V	1.724	1.00
54_L	62_A	1.701	1.00
55_E	58_G	1.657	1.00
8_R	28_R	1.537	1.00
9_F	13_L	1.476	1.00
58_G	62_A	1.426	1.00
26_R	77_E	1.407	1.00
48_T	60_L	1.401	1.00
64_V	69_F	1.394	1.00
4_V	8_R	1.393	1.00
53_T	56_S	1.382	1.00
13_L	16_R	1.379	1.00
51_V	56_S	1.368	1.00
23_R	27_L	1.359	1.00
4_V	28_R	1.316	1.00
59_V	62_A	1.275	1.00
40_L	49_V	1.213	1.00
61_G	65_L	1.207	1.00
68_T	73_F	1.200	1.00
33_L	40_L	1.173	1.00
9_F	32_A	1.145	1.00
7_V	11_R	1.137	1.00
14_L	17_R	1.115	1.00
65_L	69_F	1.109	1.00
24_R	28_R	1.038	1.00
12_R	17_R	1.000	1.00
47_R	56_S	0.980	1.00
50_A	56_S	0.980	1.00
11_R	14_L	0.969	1.00
2_A	39_F	0.954	1.00
54_L	59_V	0.939	1.00
33_L	44_D	0.927	1.00
52_P	59_V	0.924	1.00
35_L	38_E	0.910	1.00
8_R	12_R	0.907	1.00
52_P	56_S	0.898	1.00
26_R	30_G	0.881	1.00
22_Y	31_R	0.880	1.00
18_R	21_A	0.874	1.00
11_R	17_R	0.873	1.00
20_D	24_R	0.869	1.00
25_L	35_L	0.868	1.00
32_A	42_A	0.859	1.00
41_V	44_D	0.858	1.00
22_Y	26_R	0.842	1.00
47_R	52_P	0.830	1.00
12_R	21_A	0.828	1.00
39_F	42_A	0.819	1.00
30_G	38_E	0.813	1.00
9_F	25_L	0.781	1.00
12_R	24_R	0.776	1.00
47_R	51_V	0.768	1.00
9_F	21_A	0.765	1.00
12_R	16_R	0.761	1.00
13_L	17_R	0.756	1.00
4_V	7_V	0.738	1.00
16_R	20_D	0.737	1.00
17_R	20_D	0.737	1.00
27_L	78_I	0.736	1.00
21_A	24_R	0.726	1.00
23_R	26_R	0.711	1.00
63_I	72_F	0.698	1.00
7_V	14_L	0.692	1.00
33_L	71_S	0.686	1.00
40_L	45_I	0.684	1.00
36_G	46_I	0.682	1.00
47_R	59_V	0.677	1.00
10_L	14_L	0.672	1.00
28_R	31_R	0.668	1.00
23_R	31_R	0.667	1.00
12_R	15_R	0.667	1.00
30_G	78_I	0.667	1.00
3_L	7_V	0.663	1.00
36_G	40_L	0.660	1.00
38_E	44_D	0.642	1.00
13_L	18_R	0.619	1.00
4_V	13_L	0.615	1.00
7_V	10_L	0.613	1.00
51_V	63_I	0.613	1.00
19_G	24_R	0.612	1.00
21_A	28_R	0.612	1.00
34_L	71_S	0.610	1.00
15_R	18_R	0.608	1.00
62_A	65_L	0.606	1.00
2_A	42_A	0.596	1.00
4_V	9_F	0.584	1.00
11_R	16_R	0.578	1.00
61_G	66_I	0.577	1.00
7_V	17_R	0.571	1.00
4_V	11_R	0.565	1.00
64_V	70_L	0.560	1.00
22_Y	35_L	0.560	1.00
32_A	39_F	0.556	1.00
37_L	45_I	0.556	1.00
46_I	56_S	0.555	1.00
6_L	9_F	0.540	1.00
28_R	32_A	0.536	1.00
6_L	10_L	0.536	1.00
68_T	71_S	0.534	1.00
57_V	63_I	0.531	1.00
15_R	21_A	0.530	1.00
34_L	38_E	0.518	1.00
40_L	48_T	0.513	1.00
44_D	63_I	0.513	1.00
16_R	19_G	0.504	0.99
5_A	32_A	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
3mk7A	1	0.3077	1.6	0.913	Contact Map
2rpaA	1	0.5385	1.6	0.913	Contact Map
4acoA	1	0	1.4	0.916	Contact Map
1oaoC	1	0.7949	1.4	0.917	Contact Map
4g1uA	2	0.9231	1.2	0.919	Contact Map
1odkA	3	0.5513	1.2	0.92	Contact Map
2nq2A	2	0.8846	1.1	0.92	Contact Map
1rh5A	1	0.1923	1.1	0.921	Contact Map
4b19A	1	0.2179	1.1	0.921	Contact Map
2kv5A	1	0.2436	1	0.923	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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