YKUL - BACSU - GREMLIN Contacts

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YKUL - CBS domain-containing protein YkuL

UniProt:	O31698	Sequences: MISLQSDQLLEATVGQFMIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPSYRLHGLIGTNMIMNSIFGLERIEFEKLDQITVEEVMLTDIPRLHINDPIMKGFGMVINNGFVCVENDEQVFEGIFTRRVVLKELNKHIRSLNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (122)
Sequences:	13267 (9526)
Seq/√Len:	862.4

ECOLI - IMDH KDSD GUTQ YFJD CORC YTFL YOAE YEGH
BACSU - YKUL CCPN ACUB YLBB YHCV YTOI IMDH YRKA YUGS MGTE YQHB YHDT YHDP
HALSA - Q9HQD0 Q9HPF4 Q9HRK9 Q9HNT8 Q9HMW8 Q9HNB6 Q9HR38 IMDH Q9HPN8 Q9HRX1 Q9HN02 Q9HHN9
SULSO - Q97U20 Q981B7 Q97U00 Q7LXY4 Q97VN1 Q97V95 Q97U50 Q97VD7 Q97Z58 Q7LXN6 Q97U23

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_N	35_H	3.014	1.00
29_V	58_H	2.196	1.00
98_H	101_D	2.195	1.00
29_V	87_E	2.148	1.00
99_I	120_N	2.116	1.00
101_D	105_K	2.097	1.00
27_V	31_N	2.085	1.00
97_L	101_D	2.070	1.00
27_V	50_V	1.982	1.00
14_V	106_G	1.973	1.00
97_L	118_V	1.969	1.00
95_P	113_N	1.931	1.00
27_V	48_I	1.928	1.00
36_A	86_V	1.920	1.00
49_P	57_L	1.862	1.00
52_D	56_R	1.848	1.00
85_T	88_E	1.829	1.00
28_Q	31_N	1.768	1.00
25_A	43_T	1.752	1.00
27_V	36_A	1.739	1.00
84_I	88_E	1.612	1.00
99_I	126_E	1.609	1.00
97_L	106_G	1.595	1.00
36_A	61_I	1.592	1.00
95_P	115_F	1.586	1.00
29_V	52_D	1.573	1.00
109_M	113_N	1.554	1.00
30_G	87_E	1.439	1.00
39_V	43_T	1.436	1.00
13_T	16_Q	1.436	1.00
36_A	48_I	1.427	1.00
15_G	99_I	1.421	1.00
32_N	35_H	1.383	1.00
38_L	42_K	1.356	1.00
28_Q	53_P	1.354	1.00
52_D	58_H	1.351	1.00
46_T	63_T	1.303	1.00
27_V	86_V	1.297	1.00
26_H	51_L	1.286	1.00
63_T	67_M	1.278	1.00
97_L	116_V	1.256	1.00
101_D	109_M	1.235	1.00
106_G	116_V	1.230	1.00
19_I	133_V	1.226	1.00
17_F	103_I	1.220	1.00
117_C	125_F	1.217	1.00
35_H	38_L	1.214	1.00
34_E	38_L	1.201	1.00
91_L	94_I	1.201	1.00
17_F	129_F	1.185	1.00
47_A	60_L	1.168	1.00
95_P	109_M	1.166	1.00
65_M	91_L	1.160	1.00
15_G	100_N	1.157	1.00
61_I	86_V	1.144	1.00
80_K	83_Q	1.143	1.00
34_E	82_D	1.111	1.00
108_G	112_N	1.109	1.00
60_L	117_C	1.104	1.00
120_N	124_V	1.092	1.00
61_I	66_I	1.091	1.00
31_N	39_V	1.090	1.00
102_P	105_K	1.086	1.00
97_L	109_M	1.086	1.00
120_N	126_E	1.073	1.00
84_I	89_V	1.069	1.00
61_I	89_V	1.065	1.00
50_V	90_M	1.065	1.00
98_H	121_D	1.061	1.00
49_P	125_F	1.056	1.00
25_A	39_V	1.050	1.00
37_L	66_I	1.045	1.00
33_L	89_V	1.012	1.00
57_L	94_I	1.010	1.00
96_R	119_E	1.008	1.00
106_G	129_F	0.997	1.00
51_L	58_H	0.973	1.00
14_V	97_L	0.971	1.00
111_I	136_K	0.964	1.00
27_V	39_V	0.961	1.00
39_V	42_K	0.952	1.00
25_A	45_Y	0.942	1.00
57_L	125_F	0.930	1.00
105_K	109_M	0.923	1.00
46_T	131_R	0.917	1.00
55_Y	124_V	0.902	1.00
45_Y	48_I	0.890	1.00
87_E	90_M	0.884	1.00
132_R	136_K	0.879	1.00
51_L	55_Y	0.878	1.00
71_F	74_E	0.873	1.00
56_R	123_Q	0.868	1.00
39_V	48_I	0.861	1.00
104_M	108_G	0.857	1.00
109_M	112_N	0.847	1.00
116_V	120_N	0.842	1.00
109_M	116_V	0.839	1.00
57_L	117_C	0.838	1.00
40_L	48_I	0.831	1.00
35_H	39_V	0.815	1.00
19_I	22_D	0.799	1.00
47_A	131_R	0.790	1.00
96_R	123_Q	0.785	1.00
82_D	85_T	0.781	1.00
33_L	37_L	0.777	1.00
129_F	134_V	0.771	1.00
47_A	62_G	0.770	1.00
67_M	71_F	0.757	1.00
28_Q	51_L	0.755	1.00
17_F	137_E	0.752	1.00
110_V	118_V	0.746	1.00
66_I	71_F	0.738	1.00
46_T	64_N	0.737	1.00
37_L	63_T	0.734	1.00
81_L	84_I	0.726	1.00
59_G	90_M	0.723	1.00
103_I	134_V	0.722	1.00
56_R	124_V	0.720	1.00
47_A	128_I	0.701	1.00
98_H	120_N	0.700	1.00
13_T	102_P	0.699	1.00
45_Y	133_V	0.690	1.00
73_L	84_I	0.688	1.00
13_T	100_N	0.672	1.00
14_V	18_M	0.669	1.00
105_K	108_G	0.665	1.00
73_L	79_E	0.661	1.00
106_G	110_V	0.655	1.00
99_I	121_D	0.651	1.00
49_P	117_C	0.649	1.00
63_T	132_R	0.649	1.00
24_V	49_P	0.646	1.00
26_H	55_Y	0.640	1.00
133_V	136_K	0.639	1.00
101_D	106_G	0.637	1.00
80_K	84_I	0.634	1.00
30_G	85_T	0.630	1.00
18_M	22_D	0.626	1.00
19_I	23_K	0.626	1.00
34_E	83_Q	0.625	1.00
46_T	49_P	0.622	1.00
98_H	119_E	0.614	1.00
18_M	127_G	0.611	1.00
25_A	48_I	0.609	1.00
31_N	48_I	0.607	1.00
33_L	61_I	0.603	1.00
69_S	72_G	0.598	1.00
14_V	129_F	0.592	1.00
110_V	131_R	0.592	1.00
69_S	89_V	0.589	1.00
60_L	91_L	0.586	1.00
41_T	73_L	0.578	1.00
131_R	135_L	0.578	1.00
36_A	40_L	0.573	1.00
117_C	128_I	0.570	1.00
111_I	135_L	0.563	1.00
110_V	116_V	0.557	1.00
72_G	81_L	0.557	1.00
46_T	132_R	0.546	1.00
49_P	58_H	0.546	1.00
56_R	122_E	0.546	1.00
123_Q	126_E	0.543	1.00
15_G	120_N	0.542	1.00
32_N	85_T	0.541	1.00
98_H	102_P	0.541	1.00
19_I	128_I	0.540	1.00
79_E	84_I	0.540	1.00
18_M	118_V	0.538	1.00
74_E	79_E	0.538	1.00
49_P	128_I	0.534	1.00
24_V	125_F	0.534	1.00
33_L	36_A	0.531	1.00
50_V	58_H	0.531	1.00
41_T	68_N	0.526	1.00
98_H	123_Q	0.525	1.00
119_E	125_F	0.517	1.00
106_G	109_M	0.515	1.00
60_L	94_I	0.514	1.00
55_Y	58_H	0.513	1.00
58_H	90_M	0.508	1.00
132_R	135_L	0.507	1.00
51_L	57_L	0.501	1.00
103_I	129_F	0.500	1.00

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
3lqnA	2	0.9388	99.9	0.239	Contact Map
3k6eA	2	0.9932	99.9	0.255	Contact Map
4cooA	2	0.9184	99.9	0.259	Contact Map
3pc3A	2	0.932	99.9	0.261	Contact Map
1yavA	2	0.932	99.9	0.261	Contact Map
2emqA	2	0.9252	99.9	0.279	Contact Map
4uuuA	2	0.9184	99.8	0.292	Contact Map
3l2bA	2	0.8299	99.8	0.305	Contact Map
2p9mA	2	0.8707	99.8	0.327	Contact Map
2nycA	2	0.8367	99.8	0.327	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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