YLAN - BACSU - GREMLIN Contacts

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YLAN - UPF0358 protein YlaN

UniProt:	O07638	Sequences: MASEMIVDHRQKAFELLKVDAEKILKLIRVQMDNLTMPQCPLYEEVLDTQMFGLSREIDFAVRLGLVDEKDGKDLLYTLERELSALHDAFTAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	93 (85)
Sequences:	194 (77)
Seq/√Len:	8.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_D	57_E	3.953	0.97
54_L	75_L	2.877	0.86
29_R	33_D	2.398	0.74
54_L	64_L	2.022	0.60
34_N	63_R	1.985	0.59
11_Q	76_L	1.969	0.58
47_L	51_M	1.915	0.56
62_V	66_L	1.910	0.56
38_P	54_L	1.909	0.56
56_R	86_L	1.891	0.55
10_R	71_D	1.871	0.54
25_L	82_E	1.790	0.51
23_K	76_L	1.698	0.47
11_Q	90_F	1.660	0.45
42_L	59_D	1.562	0.41
28_I	86_L	1.551	0.41
16_L	56_R	1.535	0.40
36_T	54_L	1.502	0.39
14_F	75_L	1.449	0.37
36_T	43_Y	1.431	0.36
35_L	61_A	1.409	0.35
43_Y	47_L	1.399	0.35
51_M	77_Y	1.379	0.34
7_V	78_T	1.305	0.31
46_V	90_F	1.241	0.29
7_V	85_A	1.237	0.29
38_P	87_H	1.199	0.28
9_H	68_D	1.185	0.27
30_V	43_Y	1.182	0.27
7_V	83_L	1.180	0.27
39_Q	50_Q	1.135	0.26
6_I	79_L	1.134	0.26
28_I	51_M	1.130	0.25
36_T	47_L	1.127	0.25
52_F	82_E	1.125	0.25
73_K	88_D	1.113	0.25
34_N	47_L	1.108	0.25
6_I	25_L	1.107	0.25
47_L	66_L	1.095	0.24
39_Q	64_L	1.071	0.24
23_K	59_D	1.067	0.23
30_V	36_T	1.060	0.23
41_P	57_E	1.053	0.23
6_I	15_E	1.035	0.23
25_L	87_H	1.022	0.22
64_L	86_L	1.017	0.22
68_D	71_D	1.012	0.22
12_K	26_K	1.004	0.22
16_L	54_L	0.986	0.21
37_M	41_P	0.977	0.21
13_A	72_G	0.973	0.21
78_T	84_S	0.972	0.21
26_K	70_K	0.968	0.21
52_F	77_Y	0.950	0.20
83_L	86_L	0.938	0.20
29_R	70_K	0.920	0.19
26_K	69_E	0.911	0.19
50_Q	87_H	0.900	0.19
18_K	67_V	0.892	0.19
30_V	66_L	0.882	0.18
18_K	71_D	0.876	0.18
10_R	19_V	0.849	0.18
55_S	58_I	0.842	0.17
74_D	78_T	0.841	0.17
21_A	88_D	0.835	0.17
32_M	89_A	0.830	0.17
58_I	90_F	0.830	0.17
30_V	47_L	0.821	0.17
6_I	71_D	0.818	0.17
13_A	28_I	0.809	0.17
22_E	78_T	0.795	0.16
14_F	83_L	0.792	0.16
6_I	69_E	0.789	0.16
36_T	89_A	0.786	0.16
18_K	78_T	0.786	0.16
33_D	65_G	0.770	0.16
42_L	83_L	0.759	0.15
85_A	90_F	0.756	0.15
52_F	71_D	0.749	0.15
39_Q	76_L	0.738	0.15
30_V	51_M	0.730	0.15
14_F	71_D	0.727	0.15
58_I	85_A	0.716	0.15
19_V	23_K	0.707	0.14
51_M	56_R	0.707	0.14
63_R	69_E	0.696	0.14
36_T	57_E	0.686	0.14
51_M	76_L	0.684	0.14
42_L	47_L	0.683	0.14
10_R	68_D	0.682	0.14
16_L	75_L	0.682	0.14
36_T	42_L	0.678	0.14
30_V	37_M	0.675	0.14
19_V	74_D	0.669	0.14
46_V	80_E	0.667	0.14
73_K	83_L	0.660	0.13
32_M	88_D	0.659	0.13
37_M	64_L	0.654	0.13
37_M	56_R	0.649	0.13
39_Q	84_S	0.641	0.13
19_V	78_T	0.637	0.13
25_L	74_D	0.630	0.13
14_F	52_F	0.630	0.13
60_F	67_V	0.622	0.13
74_D	77_Y	0.608	0.12
28_I	57_E	0.604	0.12
54_L	76_L	0.604	0.12
12_K	23_K	0.600	0.12
28_I	81_R	0.591	0.12
54_L	58_I	0.590	0.12
84_S	89_A	0.589	0.12
43_Y	73_K	0.585	0.12
36_T	87_H	0.584	0.12
68_D	85_A	0.581	0.12
26_K	66_L	0.564	0.12
11_Q	56_R	0.563	0.12
68_D	81_R	0.561	0.12
6_I	9_H	0.559	0.12
25_L	59_D	0.558	0.12
29_R	85_A	0.552	0.11
79_L	84_S	0.542	0.11
15_E	78_T	0.540	0.11
14_F	69_E	0.533	0.11
16_L	64_L	0.530	0.11
9_H	34_N	0.519	0.11
37_M	87_H	0.515	0.11
37_M	52_F	0.509	0.11
6_I	10_R	0.500	0.11

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
2gboA	4	0.8817	100	0.072	Contact Map
2odmA	2	0.9032	100	0.077	Contact Map
3iyuX	3	0.4301	27.6	0.925	Contact Map
3fzvA	4	0.6022	11.2	0.938	Contact Map
3czgA	1	0.4301	8.6	0.941	Contact Map
1zkrA	2	0.5914	7.8	0.942	Contact Map
3r4vA	1	0.8925	7	0.943	Contact Map
3o2tA	1	0.8925	7	0.943	Contact Map
1vw41	1	0.8602	6.9	0.943	Contact Map
1twfA	1	0.6882	6.7	0.943	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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