YOED - BACSU - GREMLIN Contacts

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YOED - Uncharacterized protein YoeD

UniProt:	O34555	Sequences: MYLTIEETAEYTNLSEDYIKSLVLEGKIRAVHDGEQFLIYKEQFKTHLEQLENYKALVQEILNEPIPEDIDVKDED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	76 (76)
Sequences:	109 (81)
Seq/√Len:	9.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_T	39_I	2.515	0.82
15_S	20_K	2.502	0.81
28_I	39_I	2.456	0.80
26_G	32_H	2.311	0.75
54_Y	62_L	2.298	0.75
6_E	16_E	2.218	0.72
42_E	45_K	2.000	0.64
24_L	32_H	1.960	0.62
57_L	61_I	1.925	0.61
23_V	35_E	1.911	0.60
18_Y	27_K	1.834	0.57
5_I	39_I	1.832	0.57
37_F	47_H	1.775	0.54
3_L	8_T	1.724	0.52
23_V	30_A	1.680	0.50
37_F	60_E	1.458	0.41
16_E	25_E	1.438	0.40
19_I	48_L	1.425	0.39
21_S	32_H	1.410	0.38
19_I	66_I	1.405	0.38
3_L	39_I	1.399	0.38
3_L	29_R	1.376	0.37
5_I	32_H	1.336	0.35
54_Y	58_V	1.285	0.33
31_V	66_I	1.268	0.33
41_K	49_E	1.247	0.32
3_L	41_K	1.192	0.30
48_L	51_L	1.191	0.30
14_L	18_Y	1.157	0.29
35_E	51_L	1.144	0.28
36_Q	49_E	1.140	0.28
23_V	42_E	1.117	0.27
11_Y	27_K	1.116	0.27
58_V	61_I	1.113	0.27
5_I	35_E	1.075	0.26
10_E	53_N	1.050	0.25
29_R	46_T	1.028	0.24
32_H	36_Q	1.025	0.24
6_E	23_V	1.016	0.24
11_Y	64_E	1.003	0.23
53_N	64_E	0.987	0.23
54_Y	57_L	0.971	0.22
19_I	46_T	0.961	0.22
8_T	26_G	0.955	0.22
32_H	56_A	0.930	0.21
41_K	53_N	0.915	0.21
41_K	47_H	0.912	0.21
18_Y	31_V	0.909	0.21
40_Y	58_V	0.905	0.20
30_A	37_F	0.901	0.20
3_L	53_N	0.886	0.20
14_L	70_I	0.884	0.20
14_L	49_E	0.874	0.20
59_Q	62_L	0.860	0.19
51_L	61_I	0.852	0.19
14_L	19_I	0.847	0.19
33_D	69_D	0.843	0.19
15_S	27_K	0.839	0.19
3_L	42_E	0.817	0.18
22_L	68_E	0.795	0.17
4_T	15_S	0.793	0.17
57_L	63_N	0.792	0.17
55_K	59_Q	0.789	0.17
14_L	51_L	0.777	0.17
4_T	11_Y	0.772	0.17
13_N	21_S	0.771	0.17
5_I	21_S	0.758	0.16
9_A	29_R	0.749	0.16
13_N	61_I	0.749	0.16
31_V	53_N	0.745	0.16
35_E	40_Y	0.731	0.16
49_E	61_I	0.730	0.16
45_K	53_N	0.727	0.16
36_Q	69_D	0.717	0.16
22_L	54_Y	0.711	0.15
16_E	68_E	0.708	0.15
18_Y	70_I	0.705	0.15
26_G	61_I	0.702	0.15
10_E	54_Y	0.702	0.15
6_E	13_N	0.690	0.15
12_T	37_F	0.683	0.15
51_L	57_L	0.673	0.15
45_K	56_A	0.670	0.14
39_I	72_V	0.655	0.14
20_K	31_V	0.655	0.14
57_L	60_E	0.646	0.14
18_Y	49_E	0.630	0.14
63_N	68_E	0.630	0.14
1_M	52_E	0.616	0.13
14_L	32_H	0.614	0.13
8_T	59_Q	0.613	0.13
16_E	56_A	0.613	0.13
26_G	49_E	0.607	0.13
54_Y	61_I	0.599	0.13
11_Y	60_E	0.596	0.13
8_T	52_E	0.592	0.13
63_N	72_V	0.582	0.13
55_K	63_N	0.580	0.13
46_T	58_V	0.578	0.13
24_L	42_E	0.575	0.13
32_H	37_F	0.565	0.12
10_E	64_E	0.564	0.12
6_E	42_E	0.558	0.12
15_S	25_E	0.553	0.12
17_D	55_K	0.551	0.12
3_L	64_E	0.551	0.12
25_E	35_E	0.550	0.12
41_K	45_K	0.542	0.12
47_H	61_I	0.540	0.12
11_Y	40_Y	0.535	0.12
6_E	45_K	0.529	0.12
30_A	73_K	0.521	0.11
6_E	26_G	0.514	0.11
22_L	72_V	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
1y6uA	1	0.6711	98.1	0.764	Contact Map
2og0A	1	0.6184	98.1	0.768	Contact Map
2kfsA	1	0.9868	96.8	0.818	Contact Map
4j2nA	4	0.6711	96.4	0.824	Contact Map
1z4hA	1	0.75	94.7	0.845	Contact Map
1j9iA	2	0.7763	94.7	0.846	Contact Map
4ua1A	2	0.8421	88.7	0.87	Contact Map
2jmlA	1	0.8553	88.6	0.87	Contact Map
1r8dA	2	0.9474	88.3	0.871	Contact Map
1pm6A	1	0.8684	86.7	0.874	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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