FER - BACSU - GREMLIN Contacts

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FER - Ferredoxin

UniProt:	P50727	Sequences: MAKYTIVDKDTCIACGACGAAAPDIYDYDDEGIAFVTLDENKGVVEVPEVLEEDMIDAFEGCPTDSIKVADEPFEGDPLKFE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	82 (75)
Sequences:	174 (108)
Seq/√Len:	12.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_Y	55_M	4.690	1.00
9_K	29_D	3.946	0.99
6_I	76_G	3.148	0.97
7_V	67_I	3.091	0.97
11_T	66_S	2.608	0.92
25_I	36_V	2.340	0.87
19_G	68_K	1.827	0.69
55_M	64_T	1.809	0.68
19_G	64_T	1.765	0.66
25_I	55_M	1.753	0.66
7_V	17_A	1.655	0.61
20_A	64_T	1.625	0.60
45_V	48_P	1.597	0.58
42_K	45_V	1.532	0.55
38_L	48_P	1.511	0.54
21_A	61_G	1.499	0.53
3_K	71_D	1.482	0.53
36_V	47_V	1.432	0.50
34_A	64_T	1.432	0.50
26_Y	52_E	1.403	0.49
17_A	21_A	1.385	0.48
5_T	26_Y	1.302	0.43
34_A	53_E	1.300	0.43
54_D	57_D	1.258	0.41
14_A	27_D	1.257	0.41
24_D	51_L	1.243	0.40
6_I	70_A	1.236	0.40
26_Y	36_V	1.191	0.38
9_K	35_F	1.189	0.38
17_A	61_G	1.146	0.36
10_D	33_I	1.102	0.34
54_D	61_G	1.085	0.33
26_Y	34_A	1.025	0.30
38_L	47_V	0.997	0.29
24_D	48_P	0.991	0.29
4_Y	24_D	0.969	0.28
19_G	65_D	0.966	0.28
42_K	47_V	0.958	0.27
31_E	68_K	0.955	0.27
8_D	28_Y	0.936	0.27
52_E	56_I	0.933	0.26
34_A	56_I	0.932	0.26
34_A	47_V	0.931	0.26
30_D	60_E	0.925	0.26
48_P	72_E	0.920	0.26
50_V	59_F	0.881	0.24
35_F	47_V	0.868	0.24
21_A	59_F	0.864	0.24
61_G	65_D	0.858	0.24
60_E	65_D	0.815	0.22
4_Y	74_F	0.805	0.22
47_V	54_D	0.799	0.21
39_D	67_I	0.779	0.21
42_K	49_E	0.769	0.20
5_T	36_V	0.746	0.20
10_D	60_E	0.743	0.20
59_F	75_E	0.738	0.19
8_D	11_T	0.733	0.19
7_V	37_T	0.729	0.19
4_Y	21_A	0.719	0.19
19_G	28_Y	0.716	0.19
28_Y	39_D	0.714	0.19
10_D	71_D	0.707	0.18
55_M	69_V	0.706	0.18
10_D	57_D	0.697	0.18
28_Y	41_N	0.687	0.18
26_Y	45_V	0.682	0.18
33_I	76_G	0.676	0.18
65_D	72_E	0.671	0.17
51_L	57_D	0.668	0.17
8_D	68_K	0.668	0.17
50_V	53_E	0.662	0.17
4_Y	19_G	0.659	0.17
30_D	69_V	0.659	0.17
40_E	49_E	0.657	0.17
41_N	67_I	0.654	0.17
44_V	69_V	0.641	0.17
34_A	49_E	0.631	0.16
14_A	32_G	0.630	0.16
28_Y	31_E	0.623	0.16
30_D	71_D	0.596	0.15
10_D	44_V	0.593	0.15
56_I	67_I	0.588	0.15
22_A	39_D	0.584	0.15
5_T	47_V	0.578	0.15
22_A	31_E	0.573	0.15
61_G	64_T	0.558	0.14
2_A	72_E	0.557	0.14
29_D	35_F	0.556	0.14
37_T	64_T	0.556	0.14
47_V	75_E	0.556	0.14
37_T	55_M	0.555	0.14
30_D	75_E	0.555	0.14
8_D	71_D	0.555	0.14
51_L	54_D	0.552	0.14
45_V	75_E	0.552	0.14
35_F	38_L	0.551	0.14
24_D	54_D	0.549	0.14
33_I	70_A	0.548	0.14
26_Y	59_F	0.543	0.14
37_T	70_A	0.543	0.14
11_T	54_D	0.537	0.14
40_E	50_V	0.532	0.14
3_K	69_V	0.528	0.14
38_L	65_D	0.527	0.14
19_G	52_E	0.518	0.13
57_D	61_G	0.510	0.13
30_D	57_D	0.510	0.13
9_K	46_E	0.505	0.13
42_K	56_I	0.503	0.13
6_I	56_I	0.502	0.13
16_G	25_I	0.500	0.13

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
1iqzA	1	0.9878	98.9	0.711	Contact Map
4id8A	1	0.7927	98.1	0.774	Contact Map
1sj1A	2	0.7927	97.9	0.785	Contact Map
1daxA	1	0.7683	97.8	0.793	Contact Map
1rofA	1	0.7317	97.4	0.806	Contact Map
1f2gA	1	0.6951	97.4	0.807	Contact Map
3i9v3	1	0.9268	97.4	0.807	Contact Map
1dwlA	1	0.7073	97.2	0.814	Contact Map
1xerA	2	0.8415	96.9	0.82	Contact Map
1gteA	4	0.8659	96.7	0.825	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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