YABA - BACSU - GREMLIN Contacts

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YABA - Initiation-control protein YabA

UniProt:	P37542	Sequences: MDKKELFDTVINLEEQIGSLYRQLGDLKQHIGEMIEENHHLQLENKHLRKRLDDTTQQIEKFKADKKESKTQKTEQTDIGEGYDNLARLYQEGFHICNVHYGSVRKEDCLFCLSFLNKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	119 (109)
Sequences:	324 (229)
Seq/√Len:	22.0

BACSU - YABA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
101_Y	104_V	4.609	1.00
100_H	110_L	3.431	1.00
83_Y	88_R	2.583	0.98
18_G	25_G	2.461	0.98
14_E	28_K	2.299	0.97
108_D	116_L	2.271	0.96
110_L	116_L	2.252	0.96
61_K	72_Q	2.194	0.96
82_G	115_F	1.868	0.90
73_K	76_Q	1.769	0.87
62_F	76_Q	1.757	0.87
20_L	91_Q	1.707	0.85
81_E	84_D	1.673	0.84
99_V	118_K	1.656	0.83
80_G	88_R	1.632	0.82
16_Q	23_Q	1.612	0.82
72_Q	75_E	1.551	0.79
18_G	21_Y	1.539	0.79
6_L	11_I	1.536	0.78
51_R	103_S	1.517	0.78
82_G	88_R	1.501	0.77
79_I	117_N	1.473	0.75
59_I	62_F	1.472	0.75
9_T	23_Q	1.439	0.74
39_H	104_V	1.425	0.73
57_Q	72_Q	1.412	0.72
100_H	103_S	1.390	0.71
31_I	34_M	1.387	0.71
4_K	8_D	1.385	0.71
79_I	116_L	1.355	0.69
96_I	116_L	1.332	0.68
14_E	92_E	1.318	0.67
81_E	88_R	1.289	0.65
30_H	33_E	1.278	0.64
3_K	38_N	1.271	0.64
35_I	43_L	1.251	0.63
88_R	115_F	1.227	0.61
16_Q	34_M	1.198	0.59
40_H	107_E	1.197	0.59
9_T	13_L	1.182	0.58
10_V	30_H	1.175	0.58
109_C	112_C	1.175	0.58
82_G	116_L	1.164	0.57
10_V	17_I	1.142	0.55
62_F	73_K	1.142	0.55
110_L	117_N	1.141	0.55
56_T	61_K	1.121	0.54
19_S	72_Q	1.116	0.54
13_L	20_L	1.108	0.53
9_T	78_D	1.107	0.53
91_Q	104_V	1.104	0.53
47_H	51_R	1.096	0.52
2_D	56_T	1.070	0.51
81_E	115_F	1.067	0.50
89_L	92_E	1.022	0.47
17_I	24_L	1.016	0.47
80_G	84_D	1.014	0.47
79_I	88_R	1.011	0.47
43_L	56_T	0.994	0.45
62_F	75_E	0.991	0.45
18_G	35_I	0.986	0.45
5_E	12_N	0.983	0.45
81_E	87_A	0.973	0.44
5_E	19_S	0.959	0.43
84_D	115_F	0.955	0.43
8_D	101_Y	0.954	0.43
114_S	118_K	0.953	0.43
29_Q	33_E	0.949	0.42
39_H	43_L	0.945	0.42
87_A	108_D	0.931	0.41
58_Q	62_F	0.929	0.41
25_G	35_I	0.927	0.41
43_L	72_Q	0.923	0.41
16_Q	118_K	0.908	0.40
27_L	35_I	0.903	0.39
79_I	87_A	0.902	0.39
55_T	60_E	0.898	0.39
27_L	89_L	0.897	0.39
87_A	115_F	0.890	0.39
58_Q	74_T	0.889	0.38
17_I	25_G	0.888	0.38
50_K	101_Y	0.877	0.38
15_E	22_R	0.872	0.37
22_R	29_Q	0.871	0.37
74_T	77_T	0.870	0.37
84_D	113_L	0.851	0.36
17_I	23_Q	0.851	0.36
79_I	96_I	0.850	0.36
60_E	76_Q	0.849	0.36
61_K	74_T	0.843	0.36
72_Q	76_Q	0.828	0.35
83_Y	96_I	0.818	0.34
96_I	117_N	0.807	0.33
91_Q	106_K	0.795	0.33
84_D	116_L	0.795	0.33
40_H	51_R	0.789	0.32
10_V	118_K	0.784	0.32
8_D	75_E	0.762	0.31
1_M	43_L	0.756	0.30
47_H	99_V	0.756	0.30
56_T	107_E	0.753	0.30
99_V	103_S	0.744	0.30
21_Y	101_Y	0.739	0.29
47_H	103_S	0.732	0.29
40_H	101_Y	0.714	0.28
46_K	50_K	0.707	0.28
3_K	101_Y	0.698	0.27
85_N	113_L	0.697	0.27
11_I	31_I	0.691	0.27
46_K	98_N	0.687	0.27
8_D	47_H	0.686	0.26
8_D	72_Q	0.686	0.26
28_K	99_V	0.674	0.26
57_Q	62_F	0.662	0.25
12_N	26_D	0.650	0.25
110_L	113_L	0.649	0.25
62_F	72_Q	0.648	0.25
82_G	108_D	0.641	0.24
32_G	47_H	0.640	0.24
22_R	26_D	0.630	0.24
88_R	96_I	0.623	0.23
28_K	108_D	0.620	0.23
31_I	99_V	0.609	0.23
21_Y	25_G	0.607	0.23
40_H	89_L	0.606	0.22
110_L	114_S	0.606	0.22
17_I	47_H	0.605	0.22
19_S	61_K	0.604	0.22
49_R	52_L	0.600	0.22
8_D	54_D	0.600	0.22
22_R	59_I	0.596	0.22
84_D	88_R	0.589	0.22
22_R	101_Y	0.586	0.22
12_N	23_Q	0.585	0.21
103_S	114_S	0.584	0.21
44_E	48_L	0.579	0.21
32_G	89_L	0.576	0.21
1_M	7_F	0.575	0.21
7_F	16_Q	0.574	0.21
73_K	77_T	0.570	0.21
19_S	50_K	0.569	0.21
8_D	15_E	0.565	0.21
106_K	118_K	0.560	0.20
33_E	57_Q	0.559	0.20
54_D	73_K	0.559	0.20
36_E	92_E	0.546	0.20
26_D	30_H	0.543	0.20
57_Q	76_Q	0.542	0.20
13_L	31_I	0.537	0.19
48_L	86_L	0.536	0.19
6_L	55_T	0.535	0.19
91_Q	114_S	0.533	0.19
40_H	106_K	0.531	0.19
22_R	25_G	0.526	0.19
80_G	110_L	0.519	0.19
3_K	7_F	0.518	0.19
59_I	73_K	0.513	0.18
29_Q	50_K	0.510	0.18
62_F	74_T	0.510	0.18
29_Q	39_H	0.509	0.18
32_G	53_D	0.508	0.18
99_V	110_L	0.504	0.18
8_D	104_V	0.500	0.18
5_E	96_I	0.500	0.18

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
3s9gA	2	0.437	86.1	0.895	Contact Map
1dipA	2	0.5966	81.7	0.9	Contact Map
3i00A	2	0.4538	71.3	0.909	Contact Map
1kd8A	1	0.2941	70.3	0.909	Contact Map
3w92A	3	0.2605	67.7	0.911	Contact Map
3c3gA	2	0.1681	63.1	0.914	Contact Map
4tl1A	2	0.2689	62.2	0.914	Contact Map
1kd8B	1	0.2941	61	0.915	Contact Map
3c3fA	3	0.1933	59.5	0.915	Contact Map
2jeeA	2	0.6555	57.7	0.916	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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