FdsD - PFAM28P - GREMLIN Contacts

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FdsD - NADH-dependant formate dehydrogenase delta subunit FdsD

PFAM:	PF11390	Sequences: KLVRMANQIAAFFASQPDREEAVAGIADHIRKFWDPRMRRQILAHLAAGGAGLDPLVREAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (60)
Sequences:	7577 (4649)
Seq/√Len:	600.2
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_D	32_K	3.110	1.00
19_R	59_E	2.604	1.00
11_A	54_D	2.292	1.00
14_A	54_D	2.246	1.00
19_R	23_V	2.156	1.00
6_A	57_V	2.055	1.00
8_Q	11_A	1.984	1.00
1_K	4_R	1.960	1.00
45_H	50_G	1.770	1.00
10_A	57_V	1.721	1.00
16_Q	21_E	1.600	1.00
11_A	14_A	1.479	1.00
40_R	44_A	1.468	1.00
26_I	56_L	1.462	1.00
4_R	8_Q	1.448	1.00
6_A	30_I	1.438	1.00
41_Q	44_A	1.411	1.00
36_P	40_R	1.387	1.00
21_E	25_G	1.323	1.00
26_I	57_V	1.319	1.00
44_A	47_A	1.274	1.00
1_K	8_Q	1.268	1.00
12_F	15_S	1.250	1.00
27_A	31_R	1.244	1.00
4_R	11_A	1.215	1.00
42_I	61_V	1.149	1.00
42_I	53_L	1.112	1.00
17_P	21_E	1.088	1.00
24_A	28_D	1.083	1.00
44_A	48_A	1.076	1.00
23_V	26_I	1.064	1.00
45_H	52_G	1.020	1.00
39_R	43_L	1.018	1.00
22_A	56_L	0.984	1.00
5_M	8_Q	0.982	1.00
46_L	58_R	0.978	1.00
25_G	28_D	0.967	1.00
54_D	57_V	0.930	1.00
43_L	61_V	0.925	1.00
20_E	24_A	0.921	1.00
24_A	27_A	0.893	1.00
16_Q	25_G	0.875	1.00
12_F	25_G	0.847	1.00
13_F	22_A	0.832	1.00
19_R	55_P	0.815	1.00
21_E	24_A	0.796	1.00
5_M	38_M	0.782	1.00
36_P	39_R	0.778	1.00
14_A	19_R	0.771	1.00
23_V	59_E	0.768	1.00
43_L	47_A	0.752	1.00
13_F	25_G	0.738	1.00
17_P	22_A	0.726	1.00
10_A	54_D	0.723	1.00
14_A	56_L	0.722	1.00
49_G	52_G	0.716	1.00
3_V	7_N	0.679	1.00
45_H	53_L	0.671	1.00
12_F	16_Q	0.657	1.00
19_R	22_A	0.653	1.00
45_H	49_G	0.650	1.00
42_I	60_A	0.647	1.00
45_H	51_A	0.645	1.00
48_A	51_A	0.630	1.00
28_D	31_R	0.621	1.00
31_R	43_L	0.621	1.00
13_F	16_Q	0.621	1.00
55_P	59_E	0.610	1.00
42_I	46_L	0.607	1.00
46_L	53_L	0.606	1.00
45_H	48_A	0.583	1.00
17_P	25_G	0.575	1.00
50_G	58_R	0.571	1.00
9_I	30_I	0.570	1.00
31_R	39_R	0.570	1.00
2_L	45_H	0.569	1.00
20_E	23_V	0.553	0.99
15_S	25_G	0.547	0.99
47_A	50_G	0.542	0.99
42_I	57_V	0.541	0.99
22_A	26_I	0.537	0.99
16_Q	22_A	0.531	0.99
2_L	5_M	0.523	0.99
10_A	26_I	0.516	0.99
41_Q	45_H	0.512	0.99
35_D	40_R	0.509	0.99
24_A	32_K	0.508	0.99
48_A	52_G	0.506	0.99
3_V	51_A	0.504	0.99
51_A	58_R	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
2vn4A	1	0.918	34.5	0.852	Contact Map
1gaiA	1	0.9016	29.2	0.857	Contact Map
2i5kA	5	0.623	24.9	0.863	Contact Map
2fbaA	1	0.9672	18.5	0.871	Contact Map
4r7pA	4	0.6557	12	0.881	Contact Map
4wodA	1	0.9836	11.9	0.881	Contact Map
3ju5A	2	0.9016	11.7	0.882	Contact Map
4nzgA	4	0.8689	10.3	0.884	Contact Map
4ae8A	2	0.623	9	0.887	Contact Map
3wfsC	1	0.9672	8.8	0.888	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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