YFEK - ECOLI - GREMLIN Contacts

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YFEK - Uncharacterized protein YfeK

UniProt:	Q47702	Sequences: MKKIICLVITLLMTLPVYAKLTAHEEARINAMLEGLAQKKDLIFVRNGDEHTCYEAVSHLRLKLGNTRNRIDTAEQFIDKVASSSSITGKPYIVKIPGKSDENAQPFLHALIAQTDKTVPAEGN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12644
Length:	124 (110)
Sequences:	140 (122)
Seq/√Len:	11.6

ECOLI - YFEK

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_R	116_D	3.618	0.99
33_L	57_V	3.611	0.99
42_L	96_I	3.123	0.96
28_R	42_L	2.951	0.95
45_V	50_E	2.559	0.89
111_L	114_Q	2.385	0.85
31_A	115_T	2.347	0.84
35_G	111_L	2.292	0.83
25_E	28_R	2.243	0.82
42_L	107_F	2.222	0.81
52_T	55_E	2.146	0.79
14_T	51_H	1.887	0.69
37_A	57_V	1.852	0.67
40_K	107_F	1.804	0.65
61_R	65_G	1.797	0.65
43_I	50_E	1.661	0.58
40_K	96_I	1.645	0.58
42_L	116_D	1.587	0.55
83_S	88_T	1.580	0.54
49_D	95_K	1.580	0.54
67_T	81_V	1.512	0.51
9_I	14_T	1.459	0.49
44_F	60_L	1.459	0.49
50_E	99_K	1.458	0.48
41_D	91_P	1.442	0.48
62_L	66_N	1.366	0.44
96_I	99_K	1.342	0.43
29_I	100_S	1.328	0.42
8_V	13_M	1.326	0.42
36_L	60_L	1.311	0.41
29_I	103_N	1.300	0.41
31_A	111_L	1.298	0.41
61_R	109_H	1.259	0.39
44_F	83_S	1.244	0.38
96_I	107_F	1.242	0.38
44_F	91_P	1.234	0.38
42_L	66_N	1.199	0.36
28_R	96_I	1.198	0.36
37_A	101_D	1.176	0.35
75_E	116_D	1.175	0.35
28_R	64_L	1.174	0.35
57_V	61_R	1.171	0.35
70_R	86_S	1.169	0.35
35_G	83_S	1.141	0.33
30_N	61_R	1.141	0.33
67_T	70_R	1.133	0.33
40_K	44_F	1.128	0.33
36_L	108_L	1.123	0.33
66_N	96_I	1.115	0.32
29_I	78_I	1.096	0.31
108_L	111_L	1.084	0.31
24_H	64_L	1.060	0.30
29_I	94_V	1.046	0.29
54_Y	84_S	1.013	0.28
74_A	97_P	1.011	0.28
60_L	67_T	0.968	0.26
57_V	68_R	0.968	0.26
40_K	78_I	0.968	0.26
33_L	108_L	0.950	0.26
67_T	86_S	0.945	0.25
20_K	54_Y	0.942	0.25
48_G	78_I	0.942	0.25
28_R	107_F	0.939	0.25
50_E	101_D	0.938	0.25
81_V	94_V	0.920	0.25
97_P	101_D	0.910	0.24
74_A	112_I	0.906	0.24
81_V	107_F	0.906	0.24
26_E	68_R	0.904	0.24
25_E	42_L	0.903	0.24
78_I	107_F	0.903	0.24
84_S	107_F	0.894	0.24
81_V	96_I	0.892	0.24
62_L	107_F	0.891	0.23
42_L	104_A	0.886	0.23
104_A	107_F	0.881	0.23
88_T	106_P	0.876	0.23
81_V	87_I	0.874	0.23
9_I	16_P	0.866	0.23
51_H	87_I	0.852	0.22
10_T	22_T	0.852	0.22
33_L	64_L	0.850	0.22
51_H	55_E	0.843	0.22
9_I	13_M	0.840	0.22
32_M	112_I	0.835	0.22
30_N	54_Y	0.833	0.21
66_N	81_V	0.830	0.21
24_H	79_D	0.822	0.21
10_T	49_D	0.820	0.21
62_L	88_T	0.815	0.21
44_F	95_K	0.815	0.21
41_D	105_Q	0.808	0.21
79_D	93_I	0.793	0.20
13_M	91_P	0.770	0.19
75_E	112_I	0.759	0.19
33_L	58_S	0.758	0.19
10_T	15_L	0.757	0.19
60_L	112_I	0.756	0.19
31_A	35_G	0.754	0.19
97_P	102_E	0.737	0.18
25_E	74_A	0.737	0.18
9_I	18_Y	0.714	0.18
10_T	24_H	0.709	0.18
62_L	83_S	0.700	0.17
74_A	88_T	0.696	0.17
65_G	73_T	0.693	0.17
28_R	75_E	0.687	0.17
54_Y	83_S	0.672	0.17
105_Q	110_A	0.671	0.17
14_T	101_D	0.667	0.16
35_G	114_Q	0.663	0.16
30_N	73_T	0.662	0.16
13_M	51_H	0.655	0.16
23_A	65_G	0.649	0.16
94_V	97_P	0.643	0.16
32_M	107_F	0.634	0.16
66_N	88_T	0.630	0.15
96_I	116_D	0.624	0.15
55_E	58_S	0.611	0.15
45_V	91_P	0.609	0.15
8_V	51_H	0.607	0.15
60_L	86_S	0.606	0.15
10_T	117_K	0.605	0.15
28_R	81_V	0.605	0.15
45_V	60_L	0.601	0.15
64_L	115_T	0.600	0.15
33_L	67_T	0.599	0.15
42_L	62_L	0.597	0.15
16_P	43_I	0.593	0.15
83_S	91_P	0.590	0.14
12_L	30_N	0.588	0.14
8_V	65_G	0.588	0.14
29_I	114_Q	0.585	0.14
67_T	80_K	0.584	0.14
35_G	94_V	0.577	0.14
44_F	67_T	0.571	0.14
7_L	11_L	0.565	0.14
45_V	62_L	0.565	0.14
15_L	19_A	0.565	0.14
76_Q	83_S	0.563	0.14
34_E	68_R	0.563	0.14
52_T	61_R	0.563	0.14
47_N	51_H	0.561	0.14
30_N	110_A	0.552	0.14
66_N	107_F	0.551	0.14
79_D	109_H	0.548	0.13
41_D	84_S	0.547	0.13
39_K	94_V	0.541	0.13
9_I	15_L	0.538	0.13
13_M	108_L	0.532	0.13
37_A	53_C	0.530	0.13
12_L	49_D	0.530	0.13
69_N	99_K	0.528	0.13
74_A	117_K	0.524	0.13
25_E	71_I	0.520	0.13
8_V	12_L	0.518	0.13
22_T	70_R	0.518	0.13
50_E	96_I	0.517	0.13
60_L	95_K	0.513	0.13
80_K	87_I	0.512	0.13
26_E	34_E	0.511	0.13
22_T	117_K	0.504	0.12
62_L	67_T	0.503	0.12
83_S	90_K	0.501	0.12
103_N	106_P	0.500	0.12

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
2esnA	3	0.9435	59.5	0.92	Contact Map
3fzvA	4	0.8871	58.9	0.92	Contact Map
2h9bA	2	0.2661	56.6	0.922	Contact Map
1ixcA	4	0.9516	54.6	0.923	Contact Map
2mmvA	2	0.3306	51.1	0.924	Contact Map
2h98A	2	0.2661	50.4	0.924	Contact Map
1al3A	1	0.2984	47.5	0.926	Contact Map
1t3uA	4	0.3629	43.8	0.927	Contact Map
3wiwA	1	0.6935	42.8	0.928	Contact Map
3fxqA	3	0.9516	42	0.928	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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