YKUS - BACSU - GREMLIN Contacts

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YKUS - UPF0180 protein YkuS

UniProt:	O34783	Sequences: MAKKIGIEQSLSDVEAALKEKGYDVVMMKSPADAQGCDCCVVTGLDNNVQGIADTVTQAPVITASGMTAEEICSEVESRIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	81 (78)
Sequences:	153 (117)
Seq/√Len:	13.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_V	47_N	5.331	1.00
14_V	72_I	4.392	1.00
39_C	76_V	2.542	0.92
75_E	79_R	2.227	0.85
23_Y	43_T	2.218	0.85
3_K	23_Y	2.090	0.82
16_A	19_K	1.824	0.72
19_K	74_S	1.771	0.69
17_A	70_E	1.767	0.69
15_E	27_M	1.720	0.67
10_S	43_T	1.714	0.67
41_V	64_A	1.708	0.66
33_D	40_C	1.581	0.60
4_K	9_Q	1.533	0.58
47_N	63_T	1.506	0.56
15_E	19_K	1.440	0.53
28_M	46_D	1.437	0.53
63_T	67_M	1.428	0.52
17_A	32_A	1.393	0.50
13_D	63_T	1.362	0.49
17_A	40_C	1.359	0.48
45_L	63_T	1.242	0.42
37_C	40_C	1.230	0.42
21_K	77_E	1.230	0.42
13_D	19_K	1.206	0.41
65_S	72_I	1.138	0.37
34_A	43_T	1.132	0.37
36_G	77_E	1.131	0.37
5_I	15_E	1.114	0.36
75_E	78_S	1.100	0.35
47_N	71_E	1.091	0.35
9_Q	51_G	1.078	0.34
13_D	32_A	1.075	0.34
4_K	16_A	1.039	0.32
28_M	59_A	1.037	0.32
46_D	61_V	1.034	0.32
3_K	7_I	0.990	0.30
54_D	80_I	0.977	0.30
67_M	75_E	0.970	0.29
25_V	72_I	0.964	0.29
3_K	28_M	0.962	0.29
50_Q	72_I	0.913	0.27
21_K	29_K	0.911	0.27
60_P	75_E	0.890	0.26
5_I	77_E	0.889	0.26
58_Q	79_R	0.887	0.26
58_Q	78_S	0.883	0.26
29_K	45_L	0.883	0.26
21_K	41_V	0.880	0.26
54_D	59_A	0.877	0.25
43_T	63_T	0.875	0.25
16_A	78_S	0.864	0.25
47_N	65_S	0.860	0.25
6_G	33_D	0.845	0.24
35_Q	70_E	0.840	0.24
24_D	71_E	0.835	0.24
19_K	55_T	0.835	0.24
19_K	30_S	0.827	0.23
10_S	54_D	0.816	0.23
32_A	78_S	0.815	0.23
39_C	70_E	0.813	0.23
29_K	52_I	0.812	0.23
17_A	23_Y	0.811	0.23
5_I	79_R	0.810	0.23
26_V	37_C	0.801	0.22
17_A	73_C	0.799	0.22
12_S	34_A	0.776	0.22
19_K	27_M	0.771	0.21
4_K	65_S	0.769	0.21
38_D	67_M	0.759	0.21
8_E	46_D	0.748	0.21
37_C	61_V	0.731	0.20
49_V	76_V	0.725	0.20
30_S	36_G	0.718	0.20
3_K	69_A	0.715	0.19
36_G	39_C	0.703	0.19
42_V	45_L	0.701	0.19
6_G	59_A	0.697	0.19
52_I	55_T	0.690	0.19
4_K	45_L	0.686	0.19
12_S	15_E	0.685	0.18
8_E	61_V	0.672	0.18
7_I	25_V	0.666	0.18
24_D	58_Q	0.664	0.18
14_V	51_G	0.643	0.17
23_Y	75_E	0.639	0.17
12_S	21_K	0.639	0.17
48_N	72_I	0.638	0.17
12_S	53_A	0.633	0.17
10_S	59_A	0.619	0.16
21_K	73_C	0.605	0.16
17_A	76_V	0.604	0.16
23_Y	57_T	0.601	0.16
25_V	67_M	0.597	0.16
17_A	51_G	0.596	0.16
29_K	34_A	0.593	0.16
6_G	40_C	0.585	0.16
45_L	55_T	0.575	0.15
33_D	37_C	0.572	0.15
65_S	70_E	0.565	0.15
28_M	32_A	0.563	0.15
15_E	32_A	0.561	0.15
29_K	33_D	0.559	0.15
12_S	16_A	0.559	0.15
15_E	61_V	0.557	0.15
21_K	67_M	0.542	0.14
39_C	74_S	0.540	0.14
7_I	59_A	0.539	0.14
20_E	75_E	0.534	0.14
19_K	50_Q	0.532	0.14
5_I	64_A	0.525	0.14
25_V	43_T	0.517	0.14
50_Q	54_D	0.516	0.14
9_Q	27_M	0.514	0.14
15_E	56_V	0.507	0.13
42_V	68_T	0.501	0.13
43_T	76_V	0.500	0.13

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
1ka9H	1	0.8148	93	0.847	Contact Map
2ywdA	1	0.8148	92.6	0.849	Contact Map
2abwA	1	0.9136	92.5	0.85	Contact Map
1q7rA	1	0.8395	90.9	0.856	Contact Map
1jvnA	1	0.8395	87.6	0.865	Contact Map
2nv0A	1	0.8272	85.8	0.868	Contact Map
2issD	1	0.8765	85.2	0.869	Contact Map
3sozA	3	0.9012	83.2	0.873	Contact Map
4gudA	1	0.8395	81.8	0.875	Contact Map
3d54D	1	0.8889	78.7	0.878	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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