YWKD - BACSU - GREMLIN Contacts

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YWKD - Uncharacterized protein YwkD

UniProt:	P45871	Sequences: MLLKSIHHIAIICSDYEKSKAFYVHKLGFQVIQETYREERGSYKLDLSLNGSYVIELFSFPDPPERQTRPEAAGLRHLAFTVGSLDKAVQELHEKGIETEPIRTDPLTGKRFTFFFDPDQLPLELYEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	128 (119)
Sequences:	3598 (1957)
Seq/√Len:	179.4

ECOLI - YAER LGUL
BACSU - YWKD YWBC YURT YQJC YETH FOSB YYAH
HALSA - Q9HQK8 Q9HRQ2
SULSO - Q97W20

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_A	25_H	5.892	1.00
90_Q	94_E	3.941	1.00
84_S	87_K	3.116	1.00
91_E	95_K	2.631	1.00
98_E	116_F	2.425	1.00
31_V	34_E	2.299	1.00
16_Y	45_L	2.295	1.00
92_L	97_I	2.064	1.00
15_D	18_K	2.029	1.00
111_R	127_E	1.980	1.00
31_V	45_L	1.911	1.00
21_A	26_K	1.854	1.00
89_V	93_H	1.791	1.00
29_F	49_L	1.771	1.00
35_T	107_L	1.766	1.00
69_R	72_A	1.757	1.00
41_G	62_D	1.698	1.00
5_S	81_T	1.649	1.00
86_D	111_R	1.640	1.00
32_I	48_S	1.626	1.00
36_Y	43_Y	1.568	1.00
93_H	99_T	1.551	1.00
88_A	91_E	1.528	1.00
24_V	30_Q	1.509	1.00
19_S	57_L	1.484	1.00
89_V	113_T	1.481	1.00
14_S	63_P	1.467	1.00
26_K	95_K	1.428	1.00
116_F	120_Q	1.424	1.00
18_K	21_A	1.365	1.00
114_F	124_E	1.317	1.00
63_P	73_A	1.308	1.00
116_F	122_P	1.285	1.00
86_D	90_Q	1.273	1.00
38_E	41_G	1.262	1.00
18_K	119_D	1.255	1.00
7_H	81_T	1.229	1.00
41_G	61_P	1.203	1.00
25_H	95_K	1.198	1.00
20_K	47_L	1.174	1.00
112_F	126_Y	1.161	1.00
93_H	101_P	1.159	1.00
113_T	125_L	1.151	1.00
43_Y	61_P	1.150	1.00
19_S	119_D	1.150	1.00
87_K	91_E	1.147	1.00
30_Q	50_N	1.141	1.00
14_S	65_E	1.114	1.00
80_F	123_L	1.112	1.00
78_L	123_L	1.110	1.00
100_E	116_F	1.085	1.00
77_H	124_E	1.081	1.00
17_E	21_A	1.080	1.00
13_C	16_Y	1.080	1.00
14_S	64_P	1.079	1.00
36_Y	41_G	1.078	1.00
87_K	90_Q	1.048	1.00
30_Q	48_S	1.047	1.00
36_Y	61_P	1.036	1.00
37_R	42_S	1.030	0.99
115_F	123_L	1.028	0.99
92_L	125_L	1.025	0.99
19_S	23_Y	1.014	0.99
90_Q	93_H	1.013	0.99
85_L	89_V	0.996	0.99
49_L	80_F	0.993	0.99
26_K	92_L	0.978	0.99
8_H	79_A	0.969	0.99
9_I	53_Y	0.962	0.99
29_F	80_F	0.945	0.99
27_L	115_F	0.939	0.99
8_H	56_E	0.935	0.99
34_E	43_Y	0.924	0.99
100_E	122_P	0.922	0.99
8_H	77_H	0.919	0.99
82_V	88_A	0.901	0.99
23_Y	117_D	0.894	0.99
42_S	60_F	0.881	0.98
104_T	107_L	0.880	0.98
85_L	111_R	0.873	0.98
7_H	126_Y	0.873	0.98
49_L	52_S	0.863	0.98
75_L	78_L	0.860	0.98
37_R	40_R	0.853	0.98
14_S	18_K	0.853	0.98
55_I	78_L	0.851	0.98
34_E	45_L	0.846	0.98
27_L	125_L	0.839	0.98
10_A	58_F	0.832	0.98
77_H	114_F	0.827	0.98
13_C	45_L	0.817	0.97
45_L	59_S	0.801	0.97
91_E	94_E	0.796	0.97
105_D	108_T	0.784	0.97
30_Q	51_G	0.777	0.97
10_A	76_R	0.776	0.97
14_S	119_D	0.763	0.96
16_Y	59_S	0.756	0.96
63_P	69_R	0.755	0.96
101_P	113_T	0.747	0.96
43_Y	59_S	0.735	0.95
35_T	44_K	0.734	0.95
51_G	54_V	0.733	0.95
12_I	121_L	0.732	0.95
62_D	65_E	0.725	0.95
115_F	125_L	0.712	0.94
71_E	74_G	0.710	0.94
97_I	115_F	0.697	0.94
89_V	99_T	0.695	0.94
69_R	116_F	0.694	0.94
26_K	97_I	0.692	0.93
44_K	58_F	0.685	0.93
11_I	23_Y	0.683	0.93
12_I	60_F	0.674	0.93
9_I	78_L	0.674	0.93
13_C	21_A	0.674	0.93
21_A	95_K	0.672	0.92
31_V	43_Y	0.665	0.92
7_H	79_A	0.663	0.92
5_S	52_S	0.662	0.92
38_E	61_P	0.659	0.92
65_E	70_P	0.658	0.92
6_I	9_I	0.650	0.91
37_R	41_G	0.649	0.91
17_E	34_E	0.648	0.91
30_Q	98_E	0.645	0.91
92_L	113_T	0.643	0.91
106_P	109_G	0.641	0.91
103_R	106_P	0.631	0.90
104_T	109_G	0.629	0.90
24_V	47_L	0.628	0.90
59_S	63_P	0.622	0.89
117_D	121_L	0.619	0.89
50_N	53_Y	0.616	0.89
19_S	118_P	0.616	0.89
99_T	115_F	0.615	0.89
89_V	98_E	0.614	0.89
42_S	105_D	0.607	0.88
36_Y	59_S	0.606	0.88
25_H	91_E	0.599	0.87
48_S	52_S	0.598	0.87
106_P	110_K	0.587	0.86
5_S	51_G	0.586	0.86
65_E	73_A	0.585	0.86
24_V	31_V	0.583	0.86
42_S	58_F	0.580	0.86
69_R	79_A	0.580	0.86
79_A	114_F	0.576	0.85
10_A	60_F	0.573	0.85
81_T	126_Y	0.573	0.85
70_P	73_A	0.571	0.85
56_E	60_F	0.560	0.84
50_N	54_V	0.560	0.84
71_E	75_L	0.557	0.83
11_I	78_L	0.557	0.83
107_L	110_K	0.553	0.83
79_A	124_E	0.553	0.83
93_H	96_G	0.552	0.83
22_F	115_F	0.551	0.83
20_K	24_V	0.549	0.83
42_S	112_F	0.540	0.82
9_I	123_L	0.540	0.82
88_A	125_L	0.537	0.81
29_F	73_A	0.536	0.81
30_Q	33_Q	0.533	0.81
13_C	59_S	0.531	0.80
85_L	112_F	0.529	0.80
6_I	11_I	0.523	0.79
72_A	79_A	0.522	0.79
101_P	108_T	0.521	0.79
86_D	104_T	0.514	0.78
19_S	117_D	0.512	0.78
37_R	44_K	0.510	0.78
33_Q	52_S	0.505	0.77
104_T	111_R	0.505	0.77
35_T	53_Y	0.504	0.77
40_R	43_Y	0.500	0.76
13_C	29_F	0.500	0.76

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
2p25A	2	0.9844	99.9	0.355	Contact Map
2c21A	2	0.9297	99.9	0.362	Contact Map
1ss4A	4	0.9922	99.9	0.363	Contact Map
3l7tA	2	0.9766	99.9	0.364	Contact Map
3w0tA	2	0.9922	99.9	0.372	Contact Map
3hdpA	2	0.9844	99.9	0.372	Contact Map
3gm5A	2	0.9766	99.9	0.381	Contact Map
1jc4A	2	1	99.9	0.382	Contact Map
4mtsA	2	0.9531	99.9	0.386	Contact Map
1f9zA	2	0.9531	99.9	0.39	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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