ACP - PFAM28P - GREMLIN Contacts

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ACP - Malonate decarboxylase delta subunit (MdcD)

PFAM:	PF06857	Sequences: KKPALAGTVESSDLEVLVEPADSGGIEIELESSVKKQFGDSIRAVIRETLERLGVKNARVSINDKGALPFVIAARLEAAVKRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	83 (80)
Sequences:	5953 (3701)
Seq/√Len:	413.8
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_R	47_R	3.363	1.00
27_E	59_R	2.413	1.00
46_I	62_I	2.356	1.00
29_E	61_S	2.338	1.00
14_L	62_I	2.039	1.00
14_L	72_I	1.998	1.00
24_G	57_N	1.818	1.00
35_K	43_R	1.818	1.00
31_E	63_N	1.786	1.00
29_E	59_R	1.731	1.00
19_E	59_R	1.721	1.00
15_E	63_N	1.712	1.00
25_G	57_N	1.692	1.00
41_S	45_V	1.659	1.00
21_A	59_R	1.629	1.00
44_A	48_E	1.590	1.00
53_L	80_V	1.532	1.00
41_S	69_P	1.486	1.00
18_V	58_A	1.428	1.00
17_L	61_S	1.403	1.00
49_T	73_A	1.320	1.00
46_I	76_L	1.319	1.00
35_K	39_G	1.316	1.00
45_V	73_A	1.299	1.00
42_I	72_I	1.274	1.00
28_I	47_R	1.270	1.00
26_I	58_A	1.269	1.00
16_V	76_L	1.243	1.00
39_G	43_R	1.236	1.00
78_A	82_R	1.230	1.00
26_I	51_E	1.215	1.00
48_E	52_R	1.193	1.00
31_E	61_S	1.182	1.00
50_L	60_V	1.171	1.00
47_R	51_E	1.155	1.00
77_E	81_K	1.133	1.00
16_V	62_I	1.131	1.00
49_T	76_L	1.128	1.00
17_L	63_N	1.109	1.00
3_P	19_E	1.106	1.00
46_I	60_V	1.086	1.00
48_E	73_A	1.056	1.00
45_V	69_P	1.024	1.00
51_E	56_K	1.002	1.00
41_S	44_A	0.999	1.00
18_V	60_V	0.988	1.00
45_V	49_T	0.986	1.00
55_V	58_A	0.984	1.00
49_T	52_R	0.952	1.00
40_D	44_A	0.941	1.00
49_T	53_L	0.938	1.00
30_L	42_I	0.938	1.00
23_S	57_N	0.921	1.00
21_A	57_N	0.921	1.00
50_L	55_V	0.919	1.00
3_P	17_L	0.910	1.00
50_L	76_L	0.869	1.00
21_A	24_G	0.868	1.00
26_I	50_L	0.859	1.00
18_V	79_A	0.839	1.00
52_R	73_A	0.836	1.00
68_L	71_V	0.798	1.00
16_V	46_I	0.793	1.00
9_V	63_N	0.786	1.00
26_I	47_R	0.781	1.00
22_D	57_N	0.778	1.00
33_S	65_K	0.772	1.00
42_I	45_V	0.769	1.00
4_A	18_V	0.762	1.00
21_A	27_E	0.760	1.00
30_L	43_R	0.757	1.00
30_L	62_I	0.757	1.00
53_L	81_K	0.743	1.00
40_D	43_R	0.737	1.00
28_I	43_R	0.736	1.00
76_L	80_V	0.731	1.00
78_A	81_K	0.724	1.00
53_L	77_E	0.721	1.00
19_E	61_S	0.718	1.00
48_E	51_E	0.711	1.00
26_I	30_L	0.708	1.00
69_P	72_I	0.706	1.00
62_I	72_I	0.703	1.00
20_P	58_A	0.698	1.00
5_L	15_E	0.698	1.00
10_E	65_K	0.678	1.00
45_V	48_E	0.676	1.00
49_T	80_V	0.672	0.99
52_R	77_E	0.665	0.99
12_S	68_L	0.664	0.99
34_V	38_F	0.659	0.99
50_L	80_V	0.655	0.99
55_V	80_V	0.650	0.99
42_I	69_P	0.637	0.99
11_S	69_P	0.637	0.99
34_V	64_D	0.621	0.99
18_V	80_V	0.617	0.99
22_D	27_E	0.613	0.99
32_S	42_I	0.602	0.99
33_S	71_V	0.601	0.99
5_L	17_L	0.596	0.99
8_T	11_S	0.592	0.99
42_I	62_I	0.587	0.99
31_E	35_K	0.579	0.99
16_V	79_A	0.577	0.98
26_I	57_N	0.575	0.98
32_S	35_K	0.569	0.98
45_V	76_L	0.558	0.98
60_V	79_A	0.549	0.98
40_D	47_R	0.542	0.98
9_V	15_E	0.538	0.98
51_E	54_G	0.533	0.97
32_S	37_Q	0.522	0.97
22_D	54_G	0.520	0.97
27_E	47_R	0.507	0.97
60_V	76_L	0.505	0.96
14_L	46_I	0.504	0.96
5_L	77_E	0.503	0.96
69_P	73_A	0.503	0.96
33_S	70_F	0.500	0.96

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
3j25A	1	1	26.4	0.877	Contact Map
4fn5A	1	0.988	24.6	0.879	Contact Map
2pokA	2	0.9639	17.3	0.888	Contact Map
2jvfA	1	0.8795	16.2	0.889	Contact Map
4mcaA	7	0.6627	12.2	0.895	Contact Map
3tx8A	2	0.9639	11.2	0.897	Contact Map
2dy1A	1	0.9518	10.4	0.898	Contact Map
3iszA	2	0.9518	10.2	0.898	Contact Map
4mmoA	2	0.9518	10.2	0.898	Contact Map
1kyfA	1	0.5904	9.6	0.9	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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