YQBM - BACSU - GREMLIN Contacts

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YQBM - Uncharacterized protein YqbM

UniProt:	P45929	Sequences: MALKAQNTISGKEGRLFLDGEEMAHIKTFEANVEKNKSEVNIMGRRMTGHKTTGANGTGTATFYKVTSQFVLIMMDYVKKGSDPYFTLQAVLDDASSGRGTERVTLYDVNFDSAKIAGLDVDSEALEEEVPFTFEDFDVPEQLKSTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (138)
Sequences:	295 (231)
Seq/√Len:	19.7

BACSU - YQBM XKDM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_G	132_F	4.097	1.00
57_G	134_F	3.143	0.99
37_K	133_T	2.955	0.99
39_E	56_N	2.933	0.99
32_N	113_S	2.885	0.99
47_M	55_A	2.878	0.99
14_G	119_L	2.870	0.99
39_E	50_H	2.783	0.99
34_E	113_S	2.617	0.98
72_L	142_Q	2.595	0.98
29_F	106_L	2.567	0.98
37_K	112_D	2.416	0.97
34_E	58_T	2.339	0.96
120_D	123_S	2.109	0.93
31_A	106_L	2.050	0.92
83_D	110_N	2.008	0.91
79_K	138_D	1.978	0.90
13_E	46_R	1.915	0.88
28_T	62_T	1.910	0.88
19_D	73_I	1.900	0.88
34_E	56_N	1.886	0.88
112_D	133_T	1.862	0.87
16_L	24_A	1.827	0.86
75_M	137_F	1.779	0.84
35_K	83_D	1.742	0.83
14_G	26_I	1.730	0.83
29_F	88_L	1.726	0.82
16_L	29_F	1.704	0.82
11_G	14_G	1.647	0.79
51_K	94_D	1.525	0.74
14_G	61_A	1.500	0.72
35_K	110_N	1.494	0.72
28_T	120_D	1.488	0.72
89_Q	140_P	1.487	0.72
60_T	131_P	1.456	0.70
79_K	136_D	1.443	0.69
38_S	129_E	1.412	0.68
94_D	100_G	1.409	0.67
116_I	137_F	1.386	0.66
30_E	118_G	1.350	0.64
36_N	54_G	1.261	0.59
107_Y	138_D	1.249	0.58
36_N	104_V	1.247	0.58
21_E	69_Q	1.241	0.57
90_A	117_A	1.193	0.54
17_F	91_V	1.192	0.54
29_F	90_A	1.190	0.54
15_R	91_V	1.187	0.54
24_A	63_F	1.164	0.52
15_R	22_E	1.160	0.52
37_K	110_N	1.145	0.51
106_L	109_V	1.141	0.51
21_E	103_R	1.133	0.50
73_I	93_D	1.115	0.49
23_M	88_L	1.111	0.49
27_K	127_E	1.108	0.49
48_T	56_N	1.108	0.49
65_K	71_V	1.077	0.47
112_D	131_P	1.070	0.46
40_V	61_A	1.063	0.46
68_S	102_E	1.051	0.45
67_T	70_F	1.045	0.45
65_K	102_E	1.038	0.44
101_T	141_E	1.036	0.44
38_S	52_T	1.022	0.43
50_H	56_N	1.019	0.43
72_L	76_D	1.013	0.43
26_I	61_A	0.980	0.41
35_K	52_T	0.977	0.41
33_V	78_V	0.976	0.40
32_N	60_T	0.965	0.40
85_Y	110_N	0.960	0.39
105_T	140_P	0.941	0.38
76_D	79_K	0.928	0.38
110_N	133_T	0.923	0.37
47_M	136_D	0.917	0.37
87_T	105_T	0.910	0.36
19_D	76_D	0.910	0.36
14_G	43_M	0.892	0.35
9_I	143_L	0.888	0.35
78_V	136_D	0.882	0.35
28_T	118_G	0.879	0.35
75_M	79_K	0.879	0.35
42_I	45_R	0.877	0.35
27_K	64_Y	0.873	0.34
93_D	101_T	0.856	0.33
113_S	130_V	0.855	0.33
11_G	123_S	0.852	0.33
102_E	143_L	0.850	0.33
92_L	102_E	0.843	0.33
49_G	85_Y	0.842	0.33
33_V	134_F	0.823	0.31
7_N	102_E	0.816	0.31
36_N	53_T	0.816	0.31
16_L	88_L	0.803	0.30
51_K	100_G	0.794	0.30
34_E	60_T	0.788	0.30
24_A	136_D	0.786	0.29
45_R	49_G	0.782	0.29
92_L	143_L	0.772	0.29
38_S	60_T	0.771	0.29
5_A	51_K	0.770	0.29
28_T	108_D	0.766	0.28
49_G	137_F	0.764	0.28
26_I	118_G	0.759	0.28
79_K	137_F	0.745	0.27
59_G	109_V	0.741	0.27
50_H	108_D	0.739	0.27
46_R	55_A	0.734	0.27
37_K	83_D	0.731	0.27
108_D	135_E	0.729	0.26
30_E	119_L	0.726	0.26
26_I	109_V	0.720	0.26
92_L	101_T	0.717	0.26
99_R	102_E	0.716	0.26
59_G	131_P	0.708	0.25
45_R	136_D	0.692	0.25
77_Y	143_L	0.685	0.24
49_G	112_D	0.683	0.24
25_H	67_T	0.679	0.24
11_G	128_E	0.678	0.24
76_D	136_D	0.678	0.24
95_A	100_G	0.676	0.24
29_F	117_A	0.675	0.24
76_D	80_K	0.674	0.24
33_V	57_G	0.672	0.24
6_Q	96_S	0.670	0.24
28_T	123_S	0.670	0.24
61_A	119_L	0.666	0.23
15_R	119_L	0.662	0.23
38_S	120_D	0.661	0.23
33_V	55_A	0.661	0.23
55_A	116_I	0.657	0.23
32_N	114_A	0.652	0.23
44_G	121_V	0.649	0.23
33_V	116_I	0.647	0.23
65_K	128_E	0.639	0.22
68_S	139_V	0.635	0.22
92_L	103_R	0.634	0.22
96_S	103_R	0.632	0.22
38_S	54_G	0.632	0.22
17_F	103_R	0.625	0.22
39_E	131_P	0.624	0.22
99_R	143_L	0.623	0.22
62_T	127_E	0.620	0.21
4_K	21_E	0.619	0.21
103_R	143_L	0.613	0.21
67_T	105_T	0.610	0.21
36_N	56_N	0.607	0.21
20_G	76_D	0.606	0.21
19_D	32_N	0.603	0.21
43_M	121_V	0.600	0.21
32_N	56_N	0.593	0.20
96_S	105_T	0.592	0.20
62_T	123_S	0.590	0.20
71_V	139_V	0.589	0.20
53_T	73_I	0.583	0.20
15_R	93_D	0.582	0.20
89_Q	101_T	0.578	0.20
47_M	57_G	0.575	0.20
39_E	47_M	0.575	0.20
35_K	135_E	0.573	0.19
55_A	128_E	0.570	0.19
7_N	19_D	0.569	0.19
76_D	125_A	0.568	0.19
28_T	32_N	0.567	0.19
14_G	129_E	0.566	0.19
24_A	116_I	0.565	0.19
78_V	116_I	0.563	0.19
27_K	62_T	0.555	0.19
112_D	135_E	0.554	0.19
26_I	132_F	0.554	0.19
53_T	80_K	0.553	0.19
6_Q	76_D	0.552	0.19
60_T	139_V	0.552	0.19
115_K	118_G	0.549	0.18
26_I	130_V	0.545	0.18
63_F	67_T	0.543	0.18
39_E	129_E	0.537	0.18
43_M	143_L	0.536	0.18
118_G	127_E	0.536	0.18
39_E	59_G	0.535	0.18
58_T	127_E	0.532	0.18
42_I	49_G	0.531	0.18
26_I	60_T	0.531	0.18
89_Q	105_T	0.530	0.18
26_I	88_L	0.528	0.18
112_D	121_V	0.527	0.18
8_T	41_N	0.526	0.18
21_E	131_P	0.525	0.18
54_G	128_E	0.524	0.18
29_F	75_M	0.522	0.17
82_S	140_P	0.518	0.17
7_N	99_R	0.518	0.17
91_V	103_R	0.518	0.17
68_S	141_E	0.516	0.17
12_K	17_F	0.516	0.17
90_A	119_L	0.516	0.17
37_K	135_E	0.515	0.17
107_Y	136_D	0.514	0.17
109_V	132_F	0.512	0.17
90_A	102_E	0.507	0.17
30_E	130_V	0.506	0.17
29_F	59_G	0.506	0.17
64_Y	121_V	0.502	0.17
49_G	135_E	0.501	0.17
66_V	95_A	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
2gujA	1	0.9048	100	0.098	Contact Map
3j9qS	11	0.932	48.1	0.931	Contact Map
3v4hA	5	0.7687	20.5	0.943	Contact Map
3wx6A	6	0.7483	19.5	0.944	Contact Map
3he1A	3	0.8231	19.3	0.944	Contact Map
4ksrA	3	0.8776	15	0.947	Contact Map
2k4qA	1	0.8912	10.4	0.95	Contact Map
4hkhA	1	0.8912	8.8	0.952	Contact Map
1y12A	3	0.9116	8.6	0.952	Contact Map
3eaaA	3	0.9116	8	0.953	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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