DUF4388 - PFAM28P - GREMLIN Contacts

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DUF4388 - Domain of unknown function (DUF4388)

PFAM:	PF14332	Sequences: SGSLSDFSLPDLLQLLALSRKTGVLTVTSGGGEGRIYFRDGRIVHAEQEALYELLSWTEGTFEFEPGEPPPERTITLSTEALLLEGARRLDEWK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (91)
Sequences:	34468 (22623)
Seq/√Len:	2371.5
META:	0.973

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_A	79_T	2.613	1.00
24_V	35_R	2.486	1.00
34_G	54_L	2.379	1.00
45_H	74_T	2.322	1.00
23_G	64_F	2.317	1.00
29_S	57_W	2.210	1.00
39_R	44_V	2.065	1.00
26_T	65_E	1.928	1.00
11_D	19_S	1.859	1.00
55_L	86_G	1.846	1.00
24_V	37_Y	1.797	1.00
26_T	35_R	1.720	1.00
52_Y	89_R	1.718	1.00
78_S	81_A	1.636	1.00
73_R	76_T	1.601	1.00
29_S	32_G	1.570	1.00
37_Y	45_H	1.562	1.00
2_G	62_F	1.556	1.00
17_A	80_E	1.553	1.00
84_L	91_D	1.550	1.00
46_A	50_A	1.479	1.00
28_T	33_E	1.477	1.00
85_E	88_R	1.474	1.00
16_L	21_K	1.457	1.00
7_F	15_L	1.446	1.00
17_A	42_R	1.361	1.00
26_T	33_E	1.359	1.00
22_T	39_R	1.340	1.00
22_T	41_G	1.283	1.00
24_V	67_G	1.272	1.00
36_I	51_L	1.269	1.00
13_L	79_T	1.268	1.00
16_L	38_F	1.256	1.00
3_S	6_D	1.229	1.00
3_S	61_T	1.220	1.00
5_S	59_E	1.212	1.00
14_Q	18_L	1.209	1.00
34_G	50_A	1.208	1.00
56_S	93_W	1.176	1.00
4_L	9_L	1.175	1.00
36_I	43_I	1.161	1.00
42_R	78_S	1.135	1.00
25_L	64_F	1.134	1.00
26_T	63_E	1.128	1.00
52_Y	86_G	1.127	1.00
9_L	27_V	1.118	1.00
84_L	87_A	1.116	1.00
20_R	40_D	1.099	1.00
28_T	61_T	1.090	1.00
8_S	11_D	1.088	1.00
51_L	82_L	1.059	1.00
34_G	53_E	1.049	1.00
39_R	73_R	1.025	1.00
4_L	60_G	0.988	1.00
21_K	64_F	0.953	1.00
42_R	79_T	0.947	1.00
36_I	54_L	0.936	1.00
43_I	79_T	0.930	1.00
53_E	56_S	0.916	1.00
58_T	90_L	0.900	1.00
15_L	19_S	0.898	1.00
24_V	65_E	0.898	1.00
65_E	68_E	0.875	1.00
28_T	63_E	0.858	1.00
21_K	66_P	0.850	1.00
88_R	92_E	0.847	1.00
56_S	90_L	0.837	1.00
81_A	85_E	0.818	1.00
35_R	48_Q	0.817	1.00
49_E	89_R	0.816	1.00
67_G	70_P	0.813	1.00
14_Q	80_E	0.807	1.00
29_S	59_E	0.806	1.00
49_E	52_Y	0.798	1.00
13_L	51_L	0.790	1.00
24_V	68_E	0.781	1.00
22_T	40_D	0.781	1.00
34_G	46_A	0.775	1.00
17_A	78_S	0.775	1.00
27_V	54_L	0.772	1.00
45_H	71_P	0.771	1.00
34_G	57_W	0.763	1.00
77_L	82_L	0.763	1.00
87_A	91_D	0.758	1.00
13_L	36_I	0.755	1.00
14_Q	84_L	0.741	1.00
30_G	59_E	0.737	1.00
77_L	81_A	0.722	1.00
52_Y	85_E	0.719	1.00
12_L	62_F	0.708	1.00
6_D	21_K	0.706	1.00
85_E	89_R	0.706	1.00
51_L	86_G	0.699	1.00
81_A	84_L	0.676	1.00
39_R	69_P	0.659	1.00
86_G	90_L	0.658	1.00
42_R	73_R	0.656	1.00
16_L	23_G	0.652	1.00
53_E	57_W	0.642	1.00
36_I	46_A	0.626	1.00
3_S	59_E	0.625	1.00
44_V	73_R	0.621	1.00
57_W	60_G	0.616	1.00
23_G	67_G	0.615	1.00
32_G	57_W	0.612	1.00
84_L	88_R	0.611	1.00
50_A	53_E	0.606	1.00
49_E	53_E	0.601	1.00
6_D	66_P	0.592	1.00
71_P	74_T	0.588	1.00
10_P	87_A	0.586	1.00
34_G	45_H	0.570	1.00
9_L	54_L	0.567	1.00
77_L	85_E	0.565	1.00
89_R	93_W	0.565	1.00
16_L	64_F	0.563	1.00
15_L	62_F	0.557	1.00
4_L	27_V	0.557	1.00
23_G	38_F	0.556	1.00
12_L	16_L	0.553	1.00
11_D	18_L	0.551	1.00
25_L	38_F	0.548	1.00
15_L	18_L	0.544	1.00
12_L	23_G	0.541	1.00
42_R	80_E	0.540	1.00
9_L	13_L	0.530	1.00
11_D	14_Q	0.525	1.00
7_F	21_K	0.524	1.00
12_L	64_F	0.519	1.00
88_R	91_D	0.518	1.00
86_G	89_R	0.515	1.00
10_P	14_Q	0.513	1.00
37_Y	71_P	0.507	1.00
13_L	38_F	0.507	1.00
81_A	88_R	0.506	1.00
11_D	15_L	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
2l48A	2	0.6596	18.1	0.857	Contact Map
2ayiA	2	0.9681	16.9	0.859	Contact Map
1zjcA	2	0.9681	15.3	0.861	Contact Map
4icsA	2	0.9681	15.3	0.861	Contact Map
3d72A	2	0.9362	10.4	0.872	Contact Map
4wujA	3	0.9681	9.8	0.873	Contact Map
4nwbA	2	0.8085	7.7	0.879	Contact Map
4hoiA	2	0.6915	7.3	0.88	Contact Map
1n9lA	2	0.6809	6.4	0.883	Contact Map
3t50A	2	0.7128	6.3	0.883	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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