YQKB - BACSU - GREMLIN Contacts

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YQKB - Uncharacterized protein YqkB

UniProt:	P54565	Sequences: MNIHVTDAAKQALQQAFDANPGKKAQLRYDAEGCGCAVSGVPTIWLAEELTGQCEQLETNGIPLYIQSSQKVFFDDQMTIDYNEKAKTLALKSPAEMLSPRMSILVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	107 (104)
Sequences:	158 (123)
Seq/√Len:	12.1

BACSU - YQKB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_D	98_L	3.844	0.99
6_T	81_D	3.831	0.99
42_P	74_F	3.759	0.99
26_Q	54_C	2.900	0.95
57_L	66_I	2.823	0.94
38_V	41_V	2.749	0.93
12_A	15_Q	2.535	0.90
92_K	102_M	2.206	0.82
66_I	74_F	2.181	0.81
99_S	102_M	1.951	0.73
47_A	65_Y	1.860	0.69
9_A	73_F	1.699	0.62
58_E	63_P	1.687	0.61
49_E	85_K	1.603	0.57
80_I	92_K	1.550	0.55
78_M	98_L	1.540	0.54
57_L	89_L	1.532	0.54
26_Q	67_Q	1.458	0.50
37_A	70_Q	1.405	0.47
94_P	98_L	1.366	0.45
79_T	89_L	1.358	0.45
59_T	69_S	1.342	0.44
80_I	104_I	1.303	0.42
6_T	9_A	1.294	0.42
30_D	38_V	1.278	0.41
5_V	25_A	1.278	0.41
33_G	91_L	1.275	0.41
83_N	94_P	1.262	0.40
9_A	91_L	1.262	0.40
26_Q	51_T	1.257	0.40
39_S	79_T	1.249	0.40
32_E	57_L	1.245	0.39
41_V	45_W	1.238	0.39
11_Q	55_E	1.228	0.39
55_E	71_K	1.218	0.38
53_Q	67_Q	1.215	0.38
74_F	84_E	1.200	0.37
90_A	99_S	1.198	0.37
52_G	68_S	1.190	0.37
30_D	35_G	1.169	0.36
18_D	52_G	1.164	0.36
13_L	93_S	1.149	0.35
59_T	94_P	1.125	0.34
26_Q	89_L	1.109	0.33
19_A	88_T	1.086	0.32
9_A	33_G	1.083	0.32
28_R	37_A	1.062	0.31
73_F	98_L	1.059	0.31
78_M	86_A	1.051	0.31
28_R	42_P	1.036	0.30
47_A	54_C	1.036	0.30
69_S	75_D	1.033	0.30
20_N	88_T	1.030	0.30
79_T	92_K	1.023	0.29
3_I	84_E	1.021	0.29
28_R	45_W	1.012	0.29
80_I	102_M	0.999	0.28
50_L	57_L	0.991	0.28
18_D	104_I	0.988	0.28
67_Q	103_S	0.980	0.28
34_C	41_V	0.975	0.27
26_Q	45_W	0.969	0.27
70_Q	102_M	0.943	0.26
41_V	72_V	0.940	0.26
22_G	46_L	0.939	0.26
4_H	68_S	0.932	0.26
4_H	8_A	0.928	0.26
38_V	78_M	0.918	0.25
9_A	72_V	0.911	0.25
11_Q	14_Q	0.907	0.25
18_D	48_E	0.906	0.25
80_I	90_A	0.905	0.25
73_F	96_E	0.899	0.24
47_A	78_M	0.882	0.24
37_A	74_F	0.880	0.24
7_D	77_Q	0.876	0.24
10_K	20_N	0.863	0.23
6_T	33_G	0.863	0.23
24_K	65_Y	0.856	0.23
44_I	75_D	0.840	0.22
32_E	49_E	0.835	0.22
4_H	19_A	0.823	0.22
21_P	58_E	0.822	0.22
27_L	35_G	0.785	0.20
55_E	104_I	0.775	0.20
66_I	98_L	0.773	0.20
48_E	85_K	0.772	0.20
65_Y	99_S	0.766	0.20
26_Q	95_A	0.754	0.19
22_G	76_D	0.753	0.19
4_H	104_I	0.752	0.19
6_T	73_F	0.747	0.19
19_A	22_G	0.747	0.19
41_V	74_F	0.742	0.19
7_D	19_A	0.723	0.19
9_A	81_D	0.720	0.18
64_L	84_E	0.716	0.18
37_A	94_P	0.715	0.18
69_S	80_I	0.702	0.18
92_K	99_S	0.697	0.18
95_A	101_R	0.687	0.17
20_N	46_L	0.674	0.17
17_F	46_L	0.672	0.17
12_A	77_Q	0.665	0.17
95_A	105_L	0.659	0.17
75_D	94_P	0.656	0.17
70_Q	98_L	0.652	0.16
37_A	95_A	0.650	0.16
38_V	42_P	0.650	0.16
44_I	98_L	0.647	0.16
47_A	77_Q	0.646	0.16
94_P	100_P	0.643	0.16
82_Y	87_K	0.634	0.16
10_K	64_L	0.633	0.16
16_A	95_A	0.624	0.16
52_G	66_I	0.608	0.15
60_N	76_D	0.608	0.15
39_S	82_Y	0.606	0.15
48_E	88_T	0.604	0.15
75_D	96_E	0.595	0.15
71_K	76_D	0.595	0.15
11_Q	49_E	0.593	0.15
25_A	102_M	0.586	0.15
51_T	89_L	0.585	0.15
46_L	79_T	0.580	0.15
16_A	25_A	0.576	0.14
21_P	99_S	0.574	0.14
12_A	57_L	0.570	0.14
90_A	102_M	0.568	0.14
7_D	13_L	0.564	0.14
2_N	77_Q	0.556	0.14
56_Q	63_P	0.553	0.14
86_A	96_E	0.551	0.14
28_R	75_D	0.544	0.14
7_D	88_T	0.539	0.14
42_P	70_Q	0.536	0.13
17_F	80_I	0.535	0.13
54_C	65_Y	0.529	0.13
44_I	72_V	0.528	0.13
83_N	95_A	0.527	0.13
31_A	39_S	0.521	0.13
56_Q	65_Y	0.520	0.13
6_T	79_T	0.520	0.13
34_C	38_V	0.520	0.13
25_A	99_S	0.517	0.13
16_A	48_E	0.514	0.13
33_G	42_P	0.513	0.13
43_T	76_D	0.513	0.13
15_Q	18_D	0.508	0.13
44_I	95_A	0.508	0.13
37_A	72_V	0.507	0.13
11_Q	54_C	0.504	0.13
51_T	70_Q	0.504	0.13
1_M	9_A	0.503	0.13
37_A	41_V	0.503	0.13
60_N	63_P	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
2qgoA	1	0.8785	99.9	0.533	Contact Map
2p2eA	1	0.9813	99.8	0.581	Contact Map
1r94A	3	0.8785	99.4	0.686	Contact Map
2d2aA	2	0.9346	99.3	0.703	Contact Map
2apnA	1	0.9439	99.2	0.713	Contact Map
1nwbA	1	0.8318	99.2	0.714	Contact Map
2k4zA	1	0.9159	99.2	0.719	Contact Map
1x0gA	4	0.9439	99	0.732	Contact Map
4g6tA	1	0.9533	39.8	0.925	Contact Map
4fj6A	4	0.5234	14.7	0.939	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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