YTKA - BACSU - GREMLIN Contacts

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YTKA - Uncharacterized protein YtkA

UniProt:	P40768	Sequences: MKKMLVVLLFSALLLNGCGSGESKANTAETPEVLDVKLTGPEKVNPGESAAYEAAVSYGDEAVTDADEVEFEVWKEGEKDASQMFKVKQEKGVYRLETTFKEDGVYTVQSHVTAKKQHSMPTLKVQVGDADAASNQSEEEHSHHH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	145 (131)
Sequences:	266 (235)
Seq/√Len:	20.5

BACSU - YTKA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_V	54_A	4.432	1.00
49_S	97_E	3.174	1.00
103_D	128_G	3.046	0.99
58_Y	115_K	2.826	0.99
34_L	58_Y	2.724	0.99
68_E	113_T	2.690	0.98
32_E	58_Y	2.683	0.98
34_L	119_S	2.446	0.97
52_Y	96_L	2.389	0.97
64_T	88_K	2.346	0.96
79_K	82_S	2.251	0.95
65_D	114_A	2.221	0.95
38_L	52_Y	2.189	0.95
38_L	112_V	2.147	0.94
74_W	109_Q	2.107	0.93
54_A	71_F	2.055	0.92
38_L	110_S	2.050	0.92
109_Q	122_T	1.942	0.90
82_S	109_Q	1.873	0.88
55_A	62_A	1.872	0.88
75_K	102_E	1.833	0.87
111_H	118_H	1.796	0.86
74_W	81_A	1.715	0.83
57_S	115_K	1.664	0.81
74_W	128_G	1.649	0.81
41_P	123_L	1.608	0.79
65_D	115_K	1.532	0.76
72_E	111_H	1.479	0.73
66_A	69_V	1.463	0.72
108_V	112_V	1.460	0.72
114_A	118_H	1.448	0.71
32_E	59_G	1.350	0.66
110_S	121_P	1.345	0.65
107_T	122_T	1.331	0.65
38_L	44_V	1.296	0.62
30_T	96_L	1.266	0.61
15_L	21_G	1.247	0.59
88_K	93_V	1.236	0.59
63_V	115_K	1.235	0.59
36_V	121_P	1.211	0.57
86_K	96_L	1.176	0.55
21_G	46_P	1.171	0.55
86_K	127_V	1.165	0.54
33_V	58_Y	1.155	0.53
10_F	17_G	1.136	0.52
54_A	110_S	1.124	0.51
74_W	107_T	1.124	0.51
23_S	84_M	1.120	0.51
66_A	114_A	1.118	0.51
81_A	109_Q	1.102	0.50
13_L	23_S	1.102	0.50
15_L	102_E	1.071	0.48
82_S	98_T	1.050	0.47
54_A	109_Q	1.046	0.46
36_V	65_D	1.045	0.46
38_L	123_L	1.043	0.46
5_L	61_E	1.036	0.46
112_V	117_Q	1.023	0.45
5_L	99_T	1.021	0.45
96_L	100_F	1.015	0.44
32_E	53_E	1.014	0.44
83_Q	109_Q	0.997	0.43
44_V	127_V	0.991	0.43
35_D	119_S	0.990	0.43
19_G	40_G	0.989	0.43
56_V	72_E	0.967	0.41
68_E	114_A	0.966	0.41
105_V	130_A	0.965	0.41
84_M	96_L	0.949	0.40
99_T	125_V	0.936	0.39
113_T	120_M	0.923	0.38
56_V	114_A	0.918	0.38
113_T	117_Q	0.904	0.37
36_V	110_S	0.900	0.37
11_S	16_N	0.900	0.37
34_L	113_T	0.869	0.35
126_Q	131_D	0.869	0.35
51_A	64_T	0.859	0.35
72_E	118_H	0.854	0.34
68_E	115_K	0.853	0.34
60_D	89_Q	0.849	0.34
109_Q	113_T	0.848	0.34
13_L	32_E	0.844	0.34
59_G	65_D	0.837	0.33
3_K	11_S	0.825	0.33
2_K	39_T	0.823	0.32
8_L	12_A	0.823	0.32
36_V	118_H	0.823	0.32
34_L	115_K	0.819	0.32
36_V	119_S	0.813	0.32
94_Y	114_A	0.806	0.32
14_L	40_G	0.800	0.31
76_E	103_D	0.798	0.31
17_G	90_E	0.792	0.31
76_E	126_Q	0.791	0.31
103_D	107_T	0.784	0.30
30_T	60_D	0.784	0.30
54_A	107_T	0.782	0.30
21_G	28_A	0.781	0.30
56_V	113_T	0.780	0.30
73_V	98_T	0.778	0.30
47_G	68_E	0.762	0.29
11_S	60_D	0.759	0.29
52_Y	100_F	0.759	0.29
30_T	58_Y	0.752	0.29
57_S	83_Q	0.752	0.29
15_L	49_S	0.749	0.28
3_K	116_K	0.749	0.28
52_Y	127_V	0.748	0.28
4_M	8_L	0.747	0.28
103_D	130_A	0.747	0.28
66_A	94_Y	0.739	0.28
19_G	131_D	0.736	0.28
47_G	95_R	0.735	0.28
15_L	34_L	0.731	0.27
33_V	52_Y	0.724	0.27
85_F	101_K	0.720	0.27
44_V	50_A	0.714	0.27
62_A	75_K	0.713	0.26
105_V	128_G	0.712	0.26
46_P	75_K	0.709	0.26
3_K	87_V	0.705	0.26
36_V	114_A	0.700	0.26
15_L	37_K	0.699	0.26
51_A	108_V	0.696	0.26
38_L	58_Y	0.694	0.26
8_L	47_G	0.691	0.25
19_G	70_E	0.686	0.25
56_V	115_K	0.681	0.25
88_K	128_G	0.677	0.25
72_E	114_A	0.674	0.25
63_V	68_E	0.673	0.24
10_F	45_N	0.671	0.24
83_Q	111_H	0.668	0.24
81_A	125_V	0.665	0.24
52_Y	95_R	0.661	0.24
17_G	42_E	0.654	0.24
54_A	121_P	0.653	0.24
46_P	128_G	0.651	0.23
55_A	84_M	0.650	0.23
90_E	97_E	0.648	0.23
77_G	105_V	0.642	0.23
9_L	54_A	0.641	0.23
32_E	55_A	0.637	0.23
110_S	123_L	0.636	0.23
86_K	102_E	0.635	0.23
14_L	35_D	0.633	0.23
53_E	59_G	0.633	0.23
117_Q	127_V	0.631	0.23
76_E	131_D	0.631	0.23
28_A	84_M	0.629	0.22
16_N	26_N	0.626	0.22
89_Q	93_V	0.625	0.22
72_E	94_Y	0.621	0.22
58_Y	107_T	0.621	0.22
113_T	118_H	0.620	0.22
44_V	125_V	0.620	0.22
8_L	14_L	0.613	0.22
2_K	126_Q	0.612	0.22
18_C	120_M	0.606	0.21
26_N	64_T	0.605	0.21
12_A	55_A	0.604	0.21
55_A	86_K	0.602	0.21
47_G	98_T	0.601	0.21
45_N	81_A	0.599	0.21
17_G	89_Q	0.596	0.21
105_V	124_K	0.586	0.21
38_L	49_S	0.585	0.20
60_D	126_Q	0.582	0.20
21_G	116_K	0.581	0.20
22_E	25_A	0.577	0.20
30_T	37_K	0.576	0.20
45_N	48_E	0.576	0.20
62_A	92_G	0.563	0.20
109_Q	112_V	0.561	0.19
4_M	55_A	0.560	0.19
55_A	117_Q	0.551	0.19
36_V	53_E	0.551	0.19
34_L	117_Q	0.542	0.19
53_E	99_T	0.539	0.19
22_E	51_A	0.536	0.18
43_K	60_D	0.536	0.18
71_F	92_G	0.533	0.18
88_K	91_K	0.530	0.18
82_S	129_D	0.521	0.18
2_K	53_E	0.519	0.18
4_M	12_A	0.512	0.18
14_L	128_G	0.511	0.17
10_F	108_V	0.511	0.17
83_Q	124_K	0.509	0.17
53_E	93_V	0.508	0.17
59_G	87_V	0.505	0.17
27_T	90_E	0.503	0.17
6_V	42_E	0.502	0.17
26_N	76_E	0.501	0.17
6_V	91_K	0.500	0.17

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
4lm8A	1	0.731	96	0.871	Contact Map
3pmqA	1	0.7448	96	0.871	Contact Map
4e9lA	1	0.8276	95.4	0.876	Contact Map
3zbiC	1	0.1931	95.3	0.878	Contact Map
2l0dA	1	0.7241	94.5	0.883	Contact Map
3iduA	1	0.7517	93.9	0.886	Contact Map
2kutA	1	0.7103	93.3	0.889	Contact Map
3c75A	1	0.6414	91.8	0.894	Contact Map
4cdgC	1	0.669	89.8	0.898	Contact Map
4lmhA	3	0.7379	89	0.9	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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