YNFD - ECOLI - GREMLIN Contacts

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YNFD - Uncharacterized protein YnfD

UniProt:	P76172	Sequences: MKLSTCCAALLLALASPAVLAAPGSCERIQSDISQRIINNGVPESSFTLSIVPNDQVDQPDSQVVGHCANDTHKILYTRTTSGNVSAPAQSSQDGAPAEPQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13842
Length:	101 (88)
Sequences:	106 (70)
Seq/√Len:	7.5

ECOLI - YNFD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_V	79_R	4.427	0.98
43_P	46_S	4.308	0.98
38_I	42_V	2.931	0.84
63_Q	71_D	2.686	0.78
62_S	76_L	2.364	0.68
13_A	32_D	1.914	0.51
18_A	53_P	1.808	0.47
62_S	73_H	1.793	0.46
54_N	63_Q	1.793	0.46
64_V	71_D	1.789	0.46
53_P	56_Q	1.786	0.46
23_P	73_H	1.716	0.43
36_R	50_S	1.657	0.41
25_S	29_I	1.601	0.39
51_I	71_D	1.578	0.38
14_L	18_A	1.561	0.38
67_H	71_D	1.490	0.35
63_Q	67_H	1.462	0.34
3_L	36_R	1.402	0.32
29_I	69_A	1.385	0.31
7_C	18_A	1.371	0.31
3_L	8_A	1.366	0.31
28_R	69_A	1.323	0.29
76_L	82_S	1.314	0.29
55_D	74_K	1.309	0.29
5_T	8_A	1.264	0.27
78_T	83_G	1.242	0.27
22_A	59_Q	1.238	0.26
24_G	28_R	1.235	0.26
16_S	21_A	1.200	0.25
32_D	38_I	1.192	0.25
10_L	13_A	1.188	0.25
51_I	67_H	1.177	0.25
28_R	36_R	1.175	0.25
3_L	6_C	1.160	0.24
76_L	80_T	1.137	0.23
52_V	74_K	1.119	0.23
6_C	62_S	1.077	0.22
85_V	89_A	1.073	0.22
21_A	35_Q	1.071	0.22
56_Q	71_D	1.069	0.22
16_S	85_V	1.068	0.22
31_S	62_S	1.067	0.22
58_D	64_V	1.050	0.21
5_T	17_P	1.045	0.21
2_K	81_T	1.029	0.21
45_S	81_T	1.026	0.20
19_V	28_R	0.996	0.20
16_S	19_V	0.982	0.19
22_A	43_P	0.968	0.19
10_L	39_N	0.961	0.19
11_L	34_S	0.950	0.19
29_I	78_T	0.943	0.18
25_S	52_V	0.937	0.18
12_L	79_R	0.935	0.18
23_P	69_A	0.928	0.18
67_H	74_K	0.924	0.18
4_S	34_S	0.922	0.18
28_R	76_L	0.914	0.18
79_R	86_S	0.908	0.18
9_A	80_T	0.895	0.17
2_K	5_T	0.883	0.17
50_S	60_P	0.881	0.17
23_P	28_R	0.870	0.17
55_D	63_Q	0.868	0.17
31_S	73_H	0.858	0.16
29_I	61_D	0.851	0.16
3_L	50_S	0.831	0.16
54_N	69_A	0.821	0.16
60_P	82_S	0.808	0.15
23_P	29_I	0.806	0.15
18_A	78_T	0.787	0.15
7_C	73_H	0.775	0.15
36_R	61_D	0.771	0.15
52_V	71_D	0.767	0.15
25_S	67_H	0.762	0.14
81_T	88_P	0.761	0.14
30_Q	46_S	0.761	0.14
2_K	83_G	0.752	0.14
24_G	73_H	0.744	0.14
11_L	38_I	0.744	0.14
52_V	55_D	0.736	0.14
18_A	21_A	0.728	0.14
34_S	45_S	0.714	0.14
29_I	70_N	0.704	0.13
15_A	80_T	0.689	0.13
6_C	14_L	0.688	0.13
15_A	24_G	0.653	0.12
80_T	84_N	0.639	0.12
20_L	45_S	0.639	0.12
48_T	70_N	0.631	0.12
27_E	38_I	0.628	0.12
52_V	58_D	0.626	0.12
2_K	8_A	0.617	0.12
7_C	23_P	0.615	0.12
82_S	86_S	0.615	0.12
35_Q	39_N	0.608	0.12
54_N	67_H	0.607	0.12
36_R	82_S	0.597	0.12
36_R	76_L	0.595	0.12
15_A	57_V	0.589	0.11
13_A	50_S	0.580	0.11
37_I	42_V	0.577	0.11
38_I	48_T	0.577	0.11
51_I	56_Q	0.575	0.11
50_S	82_S	0.574	0.11
86_S	89_A	0.571	0.11
5_T	31_S	0.570	0.11
31_S	84_N	0.568	0.11
8_A	73_H	0.567	0.11
34_S	48_T	0.565	0.11
16_S	35_Q	0.563	0.11
30_Q	35_Q	0.561	0.11
15_A	21_A	0.554	0.11
52_V	65_V	0.549	0.11
31_S	60_P	0.548	0.11
6_C	28_R	0.546	0.11
80_T	83_G	0.539	0.11
7_C	17_P	0.537	0.11
47_F	56_Q	0.530	0.11
50_S	76_L	0.530	0.11
18_A	87_A	0.517	0.10
10_L	89_A	0.515	0.10
55_D	67_H	0.514	0.10
13_A	17_P	0.513	0.10
13_A	88_P	0.511	0.10
38_I	53_P	0.509	0.10
23_P	70_N	0.509	0.10
10_L	27_E	0.506	0.10
6_C	18_A	0.506	0.10
12_L	80_T	0.500	0.10
19_V	62_S	0.500	0.10

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
2jnaA	2	0.8812	56	0.92	Contact Map
3tdgA	2	0.6337	20.4	0.937	Contact Map
3nb3A	2	0.396	18.7	0.938	Contact Map
4ivkA	4	0.5446	15.4	0.94	Contact Map
3zbiC	1	0.2673	14.5	0.941	Contact Map
4mxgA	1	0.6535	12.6	0.943	Contact Map
3oa8B	3	0.5842	12.5	0.943	Contact Map
3hunA	1	0.6238	12.4	0.943	Contact Map
2pjhA	1	0.7327	10.2	0.945	Contact Map
3bxwB	2	0.6337	8.6	0.947	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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