DUF2148 - PFAM28P - GREMLIN Contacts

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DUF2148 - Uncharacterized protein containing a ferredoxin domain (DUF2148)

PFAM:	PF09918	Sequences: KGPPCAFNLIDLGIALGSAVKTAADLNVDNRIMYSIGVAARKLGLLGEVDIVYGIPLSATGKNPFFDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (67)
Sequences:	2605 (1120)
Seq/√Len:	136.9
META:	0.948

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_I	53_Y	3.481	1.00
41_R	52_V	2.974	1.00
36_I	54_G	2.698	1.00
16_L	32_I	2.665	1.00
22_T	26_L	2.651	1.00
21_K	27_N	2.312	1.00
46_L	49_V	2.128	1.00
20_V	55_I	2.120	1.00
46_L	52_V	1.837	1.00
33_M	36_I	1.834	1.00
4_P	9_L	1.832	1.00
22_T	25_D	1.763	1.00
28_V	57_L	1.760	1.00
37_G	54_G	1.562	1.00
9_L	51_I	1.494	1.00
24_A	27_N	1.494	1.00
33_M	56_P	1.481	1.00
3_P	38_V	1.466	1.00
21_K	25_D	1.441	1.00
10_I	14_I	1.438	1.00
3_P	8_N	1.413	1.00
6_A	9_L	1.393	1.00
38_V	41_R	1.390	1.00
22_T	27_N	1.347	1.00
32_I	53_Y	1.307	1.00
44_G	48_E	1.290	1.00
28_V	59_A	1.274	1.00
2_G	5_C	1.188	1.00
39_A	43_L	1.161	0.99
38_V	42_K	1.133	0.99
58_S	64_P	1.131	0.99
5_C	11_D	1.115	0.99
10_I	16_L	1.092	0.99
4_P	8_N	1.059	0.99
20_V	32_I	0.915	0.97
30_N	57_L	0.905	0.97
23_A	30_N	0.893	0.97
62_K	67_D	0.891	0.96
8_N	35_S	0.883	0.96
17_G	32_I	0.880	0.96
7_F	53_Y	0.877	0.96
21_K	24_A	0.864	0.96
16_L	53_Y	0.833	0.95
19_A	23_A	0.790	0.93
58_S	65_F	0.762	0.92
13_G	17_G	0.758	0.92
47_G	50_D	0.750	0.91
41_R	51_I	0.746	0.91
4_P	50_D	0.728	0.90
40_A	46_L	0.728	0.90
16_L	20_V	0.704	0.89
27_N	30_N	0.697	0.88
29_D	62_K	0.694	0.88
11_D	34_Y	0.693	0.88
7_F	34_Y	0.677	0.87
34_Y	38_V	0.674	0.86
6_A	51_I	0.669	0.86
20_V	30_N	0.661	0.85
12_L	51_I	0.655	0.85
60_T	64_P	0.654	0.85
39_A	42_K	0.650	0.84
40_A	45_L	0.650	0.84
11_D	15_A	0.642	0.84
35_S	39_A	0.637	0.83
8_N	26_L	0.632	0.83
25_D	35_S	0.626	0.82
29_D	47_G	0.610	0.80
64_P	67_D	0.608	0.80
15_A	18_S	0.602	0.79
24_A	63_N	0.600	0.79
19_A	27_N	0.580	0.77
63_N	67_D	0.579	0.77
62_K	65_F	0.574	0.76
3_P	49_V	0.573	0.76
16_L	19_A	0.571	0.76
31_R	68_R	0.561	0.75
41_R	48_E	0.548	0.73
44_G	51_I	0.542	0.72
41_R	50_D	0.542	0.72
63_N	66_F	0.542	0.72
4_P	64_P	0.542	0.72
12_L	61_G	0.541	0.72
8_N	11_D	0.539	0.72
49_V	52_V	0.536	0.71
47_G	51_I	0.535	0.71
18_S	55_I	0.533	0.71
7_F	42_K	0.532	0.71
6_A	50_D	0.529	0.70
8_N	22_T	0.525	0.70
31_R	54_G	0.521	0.69
8_N	61_G	0.519	0.69
18_S	62_K	0.517	0.68
37_G	61_G	0.515	0.68
11_D	35_S	0.513	0.68
30_N	54_G	0.513	0.68
46_L	50_D	0.509	0.67
6_A	10_I	0.506	0.67
42_K	51_I	0.504	0.67
10_I	52_V	0.501	0.66
17_G	40_A	0.500	0.66

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
3n2sA	2	1	35.6	0.879	Contact Map
2wzvA	2	0.9853	35.6	0.879	Contact Map
1zchA	2	1	32.2	0.882	Contact Map
2ymvA	1	0.8824	29.5	0.884	Contact Map
3gb5A	2	0.9118	22.6	0.89	Contact Map
3e10A	2	0.9706	21.5	0.891	Contact Map
3gagA	4	1	21	0.892	Contact Map
3gr3A	2	1	19.8	0.893	Contact Map
3of4A	3	1	19.6	0.893	Contact Map
1f5vA	2	1	17.6	0.896	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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