YMAC - BACSU - GREMLIN Contacts

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YMAC - UPF0714 protein YmaC

UniProt:	O31789	Sequences: MRRFLLNVILVLAIVLFLRYVHYSLEPEPSNQPDTYSNFSSLAENESPADYDISYNEKKGSKVLIMSPHGGRIEGGVSELVRYFNNEYSTYLFEGLKSHDNQTLHITSTNFDEPLAKKKIKEHQYVVAFHGYKGENKNTLVGGTDRKRAKMIVRALERRGFSAELASSKSGLAGLNAENINNQGETGLSIQLEISREQREAFFDDFYYKNRKYTKNSEFYAYVSAIKGVLEKEYS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	235 (197)
Sequences:	179 (149)
Seq/√Len:	10.6

BACSU - YMAC YNDL YOQZ YJQB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
139_T	222_Y	5.437	1.00
198_Q	222_Y	4.110	0.99
46_E	97_K	4.080	0.99
97_K	103_T	3.777	0.99
139_T	198_Q	3.414	0.97
68_P	140_L	2.773	0.91
126_V	184_G	2.694	0.90
91_Y	111_F	2.676	0.89
95_G	101_N	2.400	0.83
134_G	195_S	2.396	0.83
132_Y	195_S	2.320	0.81
67_S	77_V	2.306	0.80
91_Y	113_E	2.297	0.80
194_I	230_L	2.232	0.78
66_M	120_I	2.129	0.75
39_F	106_I	2.124	0.74
127_V	148_R	2.123	0.74
68_P	81_V	2.116	0.74
97_K	106_I	2.077	0.73
41_S	45_N	1.993	0.69
91_Y	114_P	1.988	0.69
68_P	128_A	1.957	0.68
68_P	169_K	1.947	0.68
66_M	116_A	1.892	0.65
78_S	174_G	1.864	0.64
85_N	90_T	1.838	0.63
64_L	126_V	1.836	0.63
40_S	106_I	1.815	0.62
78_S	94_E	1.812	0.62
64_L	181_N	1.800	0.61
67_S	81_V	1.782	0.60
156_L	161_F	1.749	0.59
144_T	189_S	1.742	0.59
46_E	51_Y	1.646	0.54
189_S	229_V	1.643	0.54
131_G	199_R	1.641	0.54
211_R	214_T	1.630	0.53
202_F	216_N	1.630	0.53
163_A	194_I	1.603	0.52
55_Y	192_L	1.520	0.48
150_K	192_L	1.509	0.48
83_Y	223_V	1.491	0.47
110_N	177_A	1.468	0.46
39_F	111_F	1.466	0.46
91_Y	156_L	1.437	0.44
76_G	79_E	1.431	0.44
145_D	186_T	1.427	0.44
116_A	180_I	1.416	0.43
63_V	127_V	1.415	0.43
181_N	189_S	1.379	0.42
140_L	169_K	1.363	0.41
72_R	99_H	1.359	0.41
51_Y	163_A	1.356	0.40
216_N	219_F	1.330	0.39
109_T	176_N	1.310	0.38
53_I	113_E	1.309	0.38
98_S	197_E	1.297	0.38
89_S	92_L	1.295	0.38
153_V	163_A	1.281	0.37
152_I	190_I	1.279	0.37
84_F	226_I	1.275	0.37
41_S	68_P	1.264	0.36
89_S	123_H	1.252	0.36
65_I	178_E	1.250	0.36
105_H	193_E	1.210	0.34
140_L	172_L	1.208	0.34
132_Y	198_Q	1.191	0.33
89_S	113_E	1.175	0.33
105_H	130_H	1.169	0.32
130_H	193_E	1.169	0.32
65_I	78_S	1.167	0.32
197_E	201_A	1.155	0.32
111_F	114_P	1.154	0.32
51_Y	92_L	1.145	0.31
96_L	170_S	1.129	0.31
52_D	108_S	1.121	0.30
149_A	229_V	1.107	0.30
57_E	141_V	1.105	0.30
39_F	91_Y	1.105	0.30
116_A	120_I	1.103	0.30
128_A	145_D	1.101	0.30
72_R	203_F	1.089	0.29
64_L	123_H	1.078	0.29
86_N	227_K	1.075	0.29
77_V	179_N	1.072	0.28
64_L	119_K	1.066	0.28
112_D	160_G	1.064	0.28
158_R	228_G	1.064	0.28
121_K	133_K	1.062	0.28
99_H	111_F	1.053	0.28
106_I	111_F	1.050	0.28
72_R	100_D	1.048	0.28
67_S	85_N	1.048	0.28
207_Y	214_T	1.044	0.27
126_V	152_I	1.025	0.27
206_F	216_N	1.025	0.27
129_F	222_Y	1.024	0.27
90_T	106_I	1.021	0.27
95_G	190_I	1.003	0.26
77_V	81_V	0.983	0.25
37_S	41_S	0.963	0.24
34_D	110_N	0.959	0.24
156_L	202_F	0.955	0.24
52_D	94_E	0.955	0.24
36_Y	161_F	0.954	0.24
225_A	229_V	0.952	0.24
117_K	195_S	0.949	0.24
141_V	163_A	0.939	0.24
103_T	106_I	0.937	0.24
36_Y	46_E	0.935	0.23
75_G	123_H	0.923	0.23
137_K	218_E	0.922	0.23
111_F	219_F	0.912	0.23
148_R	189_S	0.906	0.23
78_S	183_Q	0.895	0.22
154_R	216_N	0.887	0.22
141_V	217_S	0.877	0.22
47_S	210_N	0.875	0.21
35_T	103_T	0.874	0.21
110_N	162_S	0.873	0.21
83_Y	183_Q	0.872	0.21
149_A	165_L	0.871	0.21
139_T	156_L	0.867	0.21
54_S	94_E	0.854	0.21
166_A	229_V	0.849	0.21
43_A	106_I	0.845	0.21
119_K	214_T	0.835	0.20
161_F	202_F	0.834	0.20
107_T	130_H	0.825	0.20
153_V	172_L	0.824	0.20
100_D	207_Y	0.822	0.20
80_L	89_S	0.821	0.20
172_L	225_A	0.820	0.20
76_G	139_T	0.818	0.20
152_I	156_L	0.817	0.20
95_G	123_H	0.817	0.20
106_I	127_V	0.816	0.20
135_E	160_G	0.809	0.19
38_N	106_I	0.809	0.19
141_V	181_N	0.808	0.19
77_V	119_K	0.803	0.19
51_Y	166_A	0.800	0.19
127_V	224_S	0.798	0.19
120_I	123_H	0.786	0.19
118_K	145_D	0.786	0.19
218_E	224_S	0.783	0.19
35_T	47_S	0.783	0.19
100_D	133_K	0.783	0.19
129_F	152_I	0.774	0.18
93_F	179_N	0.762	0.18
51_Y	116_A	0.761	0.18
33_P	187_G	0.759	0.18
189_S	206_F	0.757	0.18
110_N	164_E	0.756	0.18
96_L	230_L	0.755	0.18
91_Y	106_I	0.753	0.18
207_Y	211_R	0.750	0.18
39_F	43_A	0.749	0.18
63_V	187_G	0.743	0.18
74_E	179_N	0.742	0.18
125_Y	188_L	0.740	0.17
198_Q	201_A	0.740	0.17
56_N	90_T	0.737	0.17
111_F	224_S	0.733	0.17
61_S	202_F	0.731	0.17
59_K	120_I	0.729	0.17
88_Y	202_F	0.723	0.17
98_S	231_E	0.720	0.17
107_T	193_E	0.713	0.17
132_Y	222_Y	0.711	0.17
66_M	126_V	0.708	0.17
54_S	82_R	0.708	0.17
174_G	191_Q	0.704	0.17
46_E	103_T	0.703	0.17
126_V	190_I	0.703	0.17
83_Y	86_N	0.701	0.16
80_L	139_T	0.700	0.16
39_F	113_E	0.699	0.16
217_S	221_A	0.699	0.16
74_E	131_G	0.699	0.16
171_G	200_E	0.698	0.16
163_A	169_K	0.694	0.16
178_E	205_D	0.694	0.16
106_I	113_E	0.691	0.16
152_I	222_Y	0.690	0.16
171_G	183_Q	0.689	0.16
67_S	84_F	0.687	0.16
52_D	95_G	0.686	0.16
201_A	230_L	0.684	0.16
97_K	101_N	0.682	0.16
106_I	161_F	0.680	0.16
44_E	210_N	0.680	0.16
153_V	212_K	0.678	0.16
212_K	230_L	0.677	0.16
220_Y	223_V	0.676	0.16
72_R	184_G	0.670	0.16
68_P	180_I	0.666	0.16
77_V	84_F	0.665	0.16
46_E	50_D	0.663	0.15
161_F	218_E	0.662	0.15
36_Y	76_G	0.661	0.15
94_E	226_I	0.659	0.15
181_N	229_V	0.657	0.15
39_F	190_I	0.657	0.15
46_E	222_Y	0.654	0.15
34_D	144_T	0.652	0.15
80_L	221_A	0.649	0.15
43_A	97_K	0.647	0.15
202_F	218_E	0.646	0.15
64_L	125_Y	0.629	0.15
76_G	97_K	0.628	0.15
80_L	202_F	0.627	0.15
169_K	195_S	0.625	0.15
82_R	229_V	0.624	0.15
61_S	151_M	0.621	0.14
90_T	189_S	0.615	0.14
127_V	226_I	0.612	0.14
119_K	159_R	0.611	0.14
202_F	210_N	0.610	0.14
80_L	129_F	0.607	0.14
34_D	107_T	0.607	0.14
126_V	221_A	0.605	0.14
120_I	126_V	0.604	0.14
51_Y	190_I	0.603	0.14
105_H	108_S	0.601	0.14
108_S	193_E	0.601	0.14
202_F	207_Y	0.600	0.14
40_S	211_R	0.599	0.14
65_I	222_Y	0.597	0.14
134_G	197_E	0.596	0.14
35_T	218_E	0.595	0.14
73_I	130_H	0.593	0.14
116_A	194_I	0.592	0.14
81_V	90_T	0.592	0.14
108_S	130_H	0.590	0.14
41_S	133_K	0.588	0.14
100_D	110_N	0.587	0.14
59_K	119_K	0.585	0.14
140_L	163_A	0.583	0.14
218_E	228_G	0.581	0.14
80_L	163_A	0.579	0.14
109_T	160_G	0.579	0.14
210_N	214_T	0.577	0.13
194_I	209_K	0.573	0.13
76_G	222_Y	0.573	0.13
127_V	210_N	0.572	0.13
81_V	145_D	0.569	0.13
48_P	63_V	0.569	0.13
56_N	156_L	0.568	0.13
106_I	112_D	0.565	0.13
161_F	221_A	0.565	0.13
48_P	78_S	0.564	0.13
210_N	221_A	0.560	0.13
39_F	94_E	0.560	0.13
152_I	179_N	0.557	0.13
75_G	180_I	0.557	0.13
192_L	228_G	0.557	0.13
62_K	158_R	0.556	0.13
67_S	90_T	0.554	0.13
198_Q	202_F	0.551	0.13
43_A	113_E	0.550	0.13
113_E	184_G	0.550	0.13
119_K	195_S	0.549	0.13
48_P	207_Y	0.548	0.13
166_A	225_A	0.546	0.13
70_G	174_G	0.541	0.13
101_N	202_F	0.539	0.13
97_K	195_S	0.537	0.13
190_I	225_A	0.537	0.13
89_S	175_L	0.537	0.13
89_S	180_I	0.535	0.13
67_S	119_K	0.533	0.13
94_E	214_T	0.531	0.13
46_E	89_S	0.530	0.12
38_N	224_S	0.528	0.12
159_R	228_G	0.526	0.12
41_S	100_D	0.526	0.12
37_S	99_H	0.525	0.12
36_Y	97_K	0.524	0.12
174_G	219_F	0.522	0.12
70_G	76_G	0.519	0.12
78_S	129_F	0.518	0.12
38_N	221_A	0.516	0.12
214_T	225_A	0.515	0.12
121_K	135_E	0.513	0.12
211_R	216_N	0.511	0.12
110_N	201_A	0.510	0.12
64_L	189_S	0.508	0.12
63_V	228_G	0.508	0.12
50_D	65_I	0.507	0.12
97_K	197_E	0.507	0.12
34_D	64_L	0.504	0.12
65_I	201_A	0.503	0.12
148_R	190_I	0.503	0.12
65_I	83_Y	0.501	0.12
159_R	176_N	0.500	0.12

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
3a9lA	2	0.8468	100	0.223	Contact Map
2odfA	2	0.7745	95.1	0.932	Contact Map
2q7sA	1	0.7362	88.7	0.944	Contact Map
3czxA	2	0.6681	59	0.957	Contact Map
3qayA	1	0.6553	42.5	0.961	Contact Map
4lq6A	1	0.6851	33.6	0.963	Contact Map
1xovA	1	0.6596	32.2	0.963	Contact Map
2ki0A	1	0.1532	22.8	0.966	Contact Map
2xdqB	2	0.5787	22.5	0.966	Contact Map
4rn7A	1	0.6638	21.3	0.966	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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