DUF4333 - PFAM28P - GREMLIN Contacts

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DUF4333 - Domain of unknown function (DUF4333)

PFAM:	PF14230	Sequences: VLVAGCSASGGGGTTTLDAAKVEKGIADQLADQYGVLKVTSVTCPDDVKVKVGATFTCTVTVDGETYTVTVTVTDVDG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	78 (72)
Sequences:	5428 (4101)
Seq/√Len:	483.3
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_T	68_T	2.840	1.00
57_T	70_T	2.443	1.00
60_V	69_V	2.292	1.00
27_A	42_V	1.813	1.00
51_K	54_A	1.774	1.00
59_T	68_T	1.661	1.00
42_V	60_V	1.618	1.00
6_C	11_G	1.572	1.00
25_G	29_Q	1.569	1.00
26_I	71_V	1.557	1.00
49_K	54_A	1.552	1.00
26_I	29_Q	1.545	1.00
6_C	12_G	1.532	1.00
52_V	76_V	1.523	1.00
28_D	32_D	1.482	1.00
19_A	23_E	1.482	1.00
59_T	66_T	1.421	1.00
48_V	54_A	1.414	1.00
14_T	49_K	1.384	1.00
25_G	28_D	1.357	1.00
29_Q	32_D	1.321	1.00
54_A	73_V	1.314	1.00
48_V	73_V	1.309	1.00
22_V	71_V	1.288	1.00
61_T	66_T	1.254	1.00
19_A	47_D	1.236	1.00
41_S	61_T	1.211	1.00
29_Q	33_Q	1.204	1.00
55_T	70_T	1.200	1.00
16_T	47_D	1.181	1.00
17_L	22_V	1.180	1.00
50_V	73_V	1.180	1.00
73_V	76_V	1.167	1.00
22_V	25_G	1.150	1.00
27_A	39_V	1.135	1.00
22_V	56_F	1.131	1.00
18_D	21_K	1.129	1.00
62_V	67_Y	1.121	1.00
45_P	56_F	1.111	1.00
31_A	38_K	1.110	1.00
60_V	67_Y	1.084	1.00
15_T	50_V	1.074	1.00
7_S	11_G	1.067	1.00
48_V	56_F	1.049	1.00
30_L	69_V	1.031	1.00
20_A	23_E	1.022	1.00
21_K	25_G	1.021	1.00
18_D	56_F	1.018	1.00
56_F	73_V	0.992	1.00
24_K	28_D	0.986	1.00
4_A	11_G	0.958	1.00
55_T	72_T	0.944	1.00
40_T	62_V	0.936	1.00
8_A	11_G	0.923	1.00
62_V	65_E	0.914	1.00
46_D	56_F	0.909	1.00
27_A	31_A	0.882	1.00
4_A	8_A	0.876	1.00
67_Y	71_V	0.865	1.00
5_G	8_A	0.849	1.00
8_A	12_G	0.847	1.00
52_V	73_V	0.846	1.00
19_A	46_D	0.845	1.00
45_P	48_V	0.840	1.00
27_A	40_T	0.821	1.00
6_C	13_G	0.786	1.00
21_K	24_K	0.786	1.00
4_A	7_S	0.759	1.00
53_G	72_T	0.744	1.00
31_A	39_V	0.738	1.00
42_V	45_P	0.732	1.00
26_I	42_V	0.717	1.00
24_K	27_A	0.711	1.00
7_S	12_G	0.696	1.00
23_E	27_A	0.696	1.00
52_V	75_D	0.694	1.00
22_V	26_I	0.675	1.00
34_Y	62_V	0.670	1.00
17_L	73_V	0.655	1.00
30_L	34_Y	0.637	1.00
45_P	57_T	0.630	1.00
5_G	12_G	0.629	1.00
29_Q	62_V	0.626	1.00
16_T	49_K	0.624	1.00
18_D	47_D	0.624	1.00
75_D	78_G	0.609	0.99
62_V	66_T	0.606	0.99
60_V	65_E	0.601	0.99
44_C	58_C	0.587	0.99
46_D	49_K	0.582	0.99
23_E	43_T	0.582	0.99
16_T	50_V	0.581	0.99
30_L	40_T	0.572	0.99
20_A	24_K	0.570	0.99
7_S	13_G	0.569	0.99
36_V	62_V	0.567	0.99
31_A	34_Y	0.564	0.99
17_L	50_V	0.564	0.99
22_V	48_V	0.563	0.99
4_A	12_G	0.554	0.99
45_P	73_V	0.553	0.99
34_Y	39_V	0.527	0.98
40_T	61_T	0.524	0.98
15_T	49_K	0.518	0.98
11_G	14_T	0.513	0.98
30_L	60_V	0.504	0.98
8_A	13_G	0.501	0.98
46_D	51_K	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
4bhrA	1	0.8846	14.4	0.823	Contact Map
3pmqA	1	0.3205	10.5	0.834	Contact Map
1s9cA	2	0.9744	5.4	0.854	Contact Map
3khpA	3	0.9615	4.3	0.862	Contact Map
4lm8A	1	0.3846	3.8	0.864	Contact Map
3l0zA	2	0.3846	3.5	0.867	Contact Map
3kh8A	2	0.9744	3.2	0.87	Contact Map
3u4gA	2	0.4487	3	0.871	Contact Map
4q53A	2	0.8846	2.9	0.872	Contact Map
3fdrA	1	0.641	2.9	0.872	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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