YPBQ - BACSU - GREMLIN Contacts

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YPBQ - Uncharacterized protein YpbQ

UniProt:	P54158	Sequences: MFWLLIAILIVQRAAEMAVARQNEQKVKKQGAIEFGESHYPYIITMHILFFLSLIAEVLLMNKQPSSWWLGIAAVILSVQIVRYWALCSLGAYWNTKILVVPGVELVKKGPYKWMKHPNYAVVILEILLIPLLYQAYVTMCLFSIFNAVLLSVRIRAEDKALQEYSVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	168 (161)
Sequences:	533 (386)
Seq/√Len:	30.4

BACSU - YPBQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_E	99_L	4.661	1.00
24_E	97_K	3.874	1.00
9_L	130_I	3.295	1.00
57_E	139_T	3.248	1.00
27_V	32_A	3.208	1.00
75_V	125_L	3.180	1.00
43_I	150_L	3.044	1.00
32_A	99_L	3.042	1.00
66_S	135_Q	2.890	1.00
124_I	151_L	2.819	1.00
89_S	109_K	2.708	1.00
98_I	157_A	2.561	1.00
46_M	150_L	2.411	0.99
93_Y	104_V	2.296	0.99
27_V	99_L	2.264	0.99
56_A	60_L	2.197	0.98
24_E	28_K	2.013	0.97
19_V	114_W	2.011	0.97
78_S	82_V	2.005	0.97
144_S	147_N	1.912	0.96
82_V	122_V	1.884	0.96
65_P	69_W	1.827	0.95
93_Y	106_L	1.753	0.94
101_V	104_V	1.704	0.93
79_V	129_L	1.687	0.93
15_A	19_V	1.675	0.92
32_A	160_K	1.644	0.92
26_K	95_N	1.632	0.91
52_L	56_A	1.591	0.90
128_L	144_S	1.572	0.90
85_W	111_P	1.569	0.90
20_A	40_Y	1.553	0.89
136_A	139_T	1.531	0.88
26_K	30_Q	1.527	0.88
57_E	136_A	1.476	0.87
72_I	129_L	1.474	0.87
26_K	92_A	1.366	0.82
6_I	55_I	1.360	0.82
64_Q	138_V	1.360	0.82
116_K	159_D	1.356	0.81
20_A	43_I	1.353	0.81
95_N	139_T	1.329	0.80
86_A	112_Y	1.329	0.80
93_Y	105_E	1.327	0.80
20_A	76_I	1.324	0.80
10_I	55_I	1.293	0.78
130_I	133_L	1.285	0.78
7_A	55_I	1.282	0.78
28_K	33_I	1.280	0.78
98_I	161_A	1.272	0.77
34_E	97_K	1.271	0.77
60_L	141_C	1.264	0.77
10_I	52_L	1.186	0.72
57_E	95_N	1.179	0.71
109_K	153_V	1.159	0.70
53_S	139_T	1.141	0.69
128_L	132_L	1.110	0.67
80_Q	96_T	1.105	0.66
76_I	84_Y	1.099	0.66
14_A	25_Q	1.091	0.65
20_A	93_Y	1.083	0.65
35_F	138_V	1.081	0.65
113_K	132_L	1.070	0.64
4_L	8_I	1.070	0.64
43_I	48_I	1.068	0.64
47_H	120_Y	1.058	0.63
45_T	60_L	1.040	0.62
98_I	150_L	1.037	0.61
138_V	142_L	1.007	0.59
72_I	93_Y	1.006	0.59
131_P	140_M	1.005	0.59
96_T	123_V	1.005	0.59
5_L	53_S	1.004	0.59
76_I	134_Y	0.999	0.58
82_V	86_A	0.990	0.58
10_I	51_F	0.983	0.57
72_I	79_V	0.977	0.57
15_A	18_A	0.965	0.56
54_L	65_P	0.959	0.55
125_L	129_L	0.951	0.55
41_P	49_L	0.945	0.54
4_L	33_I	0.931	0.53
86_A	95_N	0.927	0.53
9_L	156_R	0.923	0.52
19_V	41_P	0.920	0.52
84_Y	122_V	0.920	0.52
27_V	95_N	0.919	0.52
125_L	128_L	0.913	0.52
43_I	46_M	0.911	0.51
37_E	152_S	0.900	0.51
17_M	87_L	0.890	0.50
155_I	160_K	0.889	0.50
32_A	58_V	0.879	0.49
68_W	148_A	0.875	0.49
16_E	80_Q	0.871	0.48
49_L	103_G	0.865	0.48
8_I	160_K	0.865	0.48
106_L	159_D	0.859	0.47
44_I	147_N	0.850	0.47
80_Q	110_G	0.835	0.45
68_W	71_G	0.833	0.45
50_F	54_L	0.826	0.45
58_V	130_I	0.820	0.44
105_E	115_M	0.808	0.43
50_F	95_N	0.807	0.43
70_L	74_A	0.803	0.43
76_I	133_L	0.801	0.43
35_F	104_V	0.799	0.43
43_I	63_K	0.798	0.42
73_A	140_M	0.793	0.42
15_A	163_Q	0.792	0.42
82_V	124_I	0.785	0.41
3_W	107_V	0.782	0.41
14_A	18_A	0.778	0.41
124_I	156_R	0.777	0.41
46_M	148_A	0.773	0.40
32_A	73_A	0.766	0.40
32_A	106_L	0.766	0.40
127_I	144_S	0.766	0.40
28_K	35_F	0.765	0.40
21_R	25_Q	0.762	0.40
47_H	119_N	0.761	0.40
16_E	110_G	0.761	0.40
146_F	150_L	0.759	0.39
79_V	122_V	0.757	0.39
89_S	110_G	0.752	0.39
8_I	81_I	0.750	0.39
43_I	153_V	0.749	0.39
146_F	160_K	0.741	0.38
87_L	98_I	0.740	0.38
145_I	160_K	0.738	0.38
7_A	146_F	0.734	0.38
102_P	112_Y	0.733	0.37
49_L	127_I	0.733	0.37
60_L	142_L	0.728	0.37
21_R	97_K	0.727	0.37
3_W	68_W	0.725	0.37
32_A	66_S	0.721	0.37
52_L	75_V	0.714	0.36
116_K	121_A	0.711	0.36
27_V	51_F	0.710	0.36
106_L	150_L	0.703	0.35
152_S	156_R	0.702	0.35
53_S	143_F	0.700	0.35
130_I	142_L	0.699	0.35
156_R	160_K	0.693	0.35
43_I	146_F	0.691	0.34
79_V	125_L	0.691	0.34
83_R	123_V	0.688	0.34
52_L	55_I	0.678	0.33
29_K	149_V	0.671	0.33
153_V	157_A	0.671	0.33
10_I	14_A	0.670	0.33
97_K	151_L	0.667	0.33
154_R	158_E	0.666	0.33
29_K	38_S	0.665	0.33
9_L	80_Q	0.663	0.32
16_E	162_L	0.663	0.32
128_L	160_K	0.662	0.32
30_Q	125_L	0.661	0.32
23_N	92_A	0.661	0.32
45_T	62_N	0.659	0.32
58_V	136_A	0.659	0.32
57_E	79_V	0.658	0.32
85_W	131_P	0.657	0.32
55_I	125_L	0.651	0.32
113_K	141_C	0.649	0.31
81_I	128_L	0.646	0.31
9_L	82_V	0.643	0.31
88_C	104_V	0.643	0.31
9_L	53_S	0.640	0.31
74_A	81_I	0.639	0.31
95_N	122_V	0.637	0.31
84_Y	101_V	0.636	0.31
16_E	96_T	0.632	0.30
115_M	121_A	0.631	0.30
69_W	115_M	0.629	0.30
62_N	163_Q	0.628	0.30
32_A	149_V	0.628	0.30
68_W	74_A	0.628	0.30
140_M	144_S	0.626	0.30
30_Q	101_V	0.626	0.30
38_S	41_P	0.623	0.30
42_Y	146_F	0.622	0.30
11_V	160_K	0.621	0.29
12_Q	51_F	0.620	0.29
116_K	133_L	0.616	0.29
15_A	74_A	0.615	0.29
40_Y	96_T	0.610	0.29
155_I	159_D	0.604	0.28
22_Q	116_K	0.604	0.28
146_F	163_Q	0.599	0.28
34_E	99_L	0.597	0.28
19_V	76_I	0.596	0.28
41_P	45_T	0.590	0.27
33_I	163_Q	0.590	0.27
5_L	132_L	0.586	0.27
129_L	135_Q	0.585	0.27
143_F	162_L	0.582	0.27
36_G	157_A	0.580	0.27
34_E	37_E	0.580	0.27
129_L	133_L	0.578	0.27
121_A	128_L	0.576	0.27
73_A	149_V	0.570	0.26
54_L	147_N	0.569	0.26
16_E	83_R	0.569	0.26
3_W	74_A	0.565	0.26
11_V	74_A	0.560	0.26
89_S	134_Y	0.557	0.25
6_I	134_Y	0.557	0.25
4_L	45_T	0.556	0.25
67_S	71_G	0.555	0.25
89_S	114_W	0.553	0.25
35_F	66_S	0.551	0.25
112_Y	122_V	0.550	0.25
100_V	162_L	0.548	0.25
54_L	134_Y	0.546	0.25
82_V	115_M	0.546	0.25
66_S	69_W	0.545	0.25
40_Y	80_Q	0.544	0.25
23_N	44_I	0.543	0.25
58_V	116_K	0.542	0.25
29_K	92_A	0.541	0.24
4_L	67_S	0.540	0.24
37_E	41_P	0.539	0.24
72_I	97_K	0.536	0.24
36_G	43_I	0.533	0.24
112_Y	130_I	0.532	0.24
75_V	129_L	0.528	0.24
124_I	144_S	0.528	0.24
89_S	111_P	0.525	0.24
108_K	113_K	0.525	0.24
116_K	136_A	0.525	0.24
54_L	79_V	0.522	0.23
5_L	86_A	0.518	0.23
19_V	150_L	0.517	0.23
29_K	88_C	0.514	0.23
6_I	57_E	0.511	0.23
12_Q	161_A	0.508	0.23
49_L	53_S	0.506	0.22
15_A	33_I	0.501	0.22
138_V	141_C	0.500	0.22

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
4a2nB	1	0.9881	99.7	0.732	Contact Map
4quvA	2	0.9821	99.2	0.803	Contact Map
2sqcA	1	0.7798	5.7	0.964	Contact Map
4ogqF	1	0.1905	2.6	0.97	Contact Map
3oiqA	2	0.3274	2.1	0.971	Contact Map
3j9pD	4	0.8512	1.9	0.972	Contact Map
1w6kA	1	0.8869	1.4	0.974	Contact Map
2mfrA	1	0.1964	1.3	0.975	Contact Map
1xwjB	1	0.1429	1.3	0.975	Contact Map
3aqpA	1	0.9702	1.2	0.975	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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