YDAH - BACSU - GREMLIN Contacts

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YDAH - Uncharacterized protein YdaH

UniProt:	P96581	Sequences: MHVITTQVLFIFCFLLLIHSIETLAYATRLSGARVGFIASALSLFNVMVIVSRMSNMVQQPFTGHLIDDAGKNALAIVGEQFRFLIFGSTVGTILGIILLPSFVALFSRAIIHLAGGGGSVFQVFRKGFSKQGFKNALSYLRLPSISYVKGFHMRLIPKRLFVINMLITSIYTIGVLSALYAGLLAPERSTTAVMASGLINGIATMLLAIFVDPKVSVLADDVAKGKRSYIYLKWTSVTMVTSRVAGTLLAQLMFIPGAYYIAWLTKWF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	269 (261)
Sequences:	197 (145)
Seq/√Len:	9.0

BACSU - YDAH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
192_T	196_A	4.328	0.99
64_G	68_D	3.576	0.96
178_S	246_A	3.335	0.94
212_V	217_S	2.903	0.89
55_S	219_L	2.838	0.88
38_I	89_S	2.774	0.86
90_T	245_V	2.706	0.85
28_T	55_S	2.671	0.84
45_F	96_G	2.576	0.82
245_V	258_G	2.501	0.80
21_I	96_G	2.435	0.78
43_S	217_S	2.427	0.78
64_G	174_I	2.305	0.74
71_G	190_S	2.295	0.74
191_T	194_V	2.198	0.70
94_I	106_L	2.193	0.70
19_H	244_R	2.113	0.67
180_L	244_R	2.087	0.66
86_I	256_I	2.087	0.66
27_A	167_L	2.082	0.66
183_G	190_S	2.039	0.64
169_T	172_Y	1.990	0.62
95_L	167_L	1.976	0.62
11_I	62_F	1.915	0.59
67_I	200_I	1.886	0.58
103_F	107_F	1.859	0.57
92_G	119_G	1.847	0.56
68_D	183_G	1.831	0.55
33_A	258_G	1.828	0.55
175_G	204_A	1.787	0.54
219_L	233_L	1.768	0.53
35_V	196_A	1.750	0.52
87_F	249_L	1.746	0.52
47_V	246_A	1.740	0.51
115_A	219_L	1.737	0.51
19_H	56_N	1.732	0.51
162_F	217_S	1.730	0.51
50_I	54_M	1.725	0.51
97_I	245_V	1.717	0.50
47_V	210_I	1.710	0.50
36_G	262_I	1.689	0.49
179_A	194_V	1.637	0.47
175_G	207_L	1.617	0.46
31_S	111_I	1.606	0.46
24_L	103_F	1.604	0.46
27_A	103_F	1.528	0.42
86_I	174_I	1.525	0.42
91_V	238_V	1.525	0.42
83_R	107_F	1.524	0.42
119_G	172_Y	1.520	0.42
45_F	110_A	1.519	0.42
253_L	256_I	1.515	0.42
48_M	170_S	1.506	0.41
53_R	208_L	1.499	0.41
46_N	96_G	1.495	0.41
114_L	198_G	1.493	0.41
135_K	159_K	1.492	0.41
60_Q	176_V	1.490	0.41
72_K	95_L	1.490	0.41
49_V	90_T	1.460	0.39
77_I	251_A	1.446	0.39
19_H	169_T	1.442	0.39
36_G	159_K	1.425	0.38
98_I	254_M	1.424	0.38
107_F	258_G	1.413	0.38
222_D	228_R	1.413	0.38
255_F	258_G	1.405	0.37
134_F	249_L	1.398	0.37
9_L	167_L	1.394	0.37
9_L	67_I	1.389	0.37
78_V	162_F	1.373	0.36
38_I	170_S	1.335	0.34
111_I	195_M	1.330	0.34
93_T	177_L	1.327	0.34
11_I	25_A	1.323	0.34
244_R	251_A	1.301	0.33
160_R	209_A	1.299	0.33
15_L	50_I	1.295	0.33
63_T	114_L	1.280	0.32
64_G	198_G	1.272	0.32
123_Q	132_Q	1.268	0.32
196_A	209_A	1.266	0.32
64_G	172_Y	1.264	0.32
141_L	178_S	1.261	0.32
36_G	143_L	1.253	0.31
62_F	227_K	1.242	0.31
33_A	220_A	1.242	0.31
55_S	103_F	1.242	0.31
13_C	135_K	1.237	0.31
21_I	45_F	1.236	0.31
17_L	166_M	1.236	0.31
159_K	209_A	1.230	0.30
183_G	196_A	1.206	0.30
143_L	149_V	1.206	0.30
136_N	212_V	1.206	0.30
142_R	146_I	1.201	0.29
19_H	176_V	1.193	0.29
24_L	61_P	1.193	0.29
114_L	186_A	1.187	0.29
86_I	255_F	1.183	0.29
115_A	223_V	1.181	0.29
34_R	221_D	1.175	0.28
16_L	95_L	1.175	0.28
107_F	255_F	1.173	0.28
33_A	39_A	1.173	0.28
178_S	258_G	1.156	0.28
226_G	234_K	1.155	0.28
71_G	217_S	1.154	0.28
104_V	111_I	1.153	0.28
25_A	217_S	1.151	0.28
10_F	129_F	1.150	0.28
67_I	167_L	1.149	0.28
167_L	231_I	1.148	0.27
106_L	253_L	1.147	0.27
53_R	200_I	1.144	0.27
63_T	196_A	1.128	0.27
83_R	252_Q	1.119	0.27
49_V	197_S	1.110	0.26
94_I	108_S	1.106	0.26
111_I	142_R	1.098	0.26
10_F	246_A	1.096	0.26
85_L	121_V	1.092	0.26
130_S	222_D	1.084	0.25
66_L	178_S	1.071	0.25
28_T	48_M	1.069	0.25
111_I	255_F	1.067	0.25
55_S	122_F	1.065	0.25
34_R	152_F	1.058	0.24
46_N	237_S	1.058	0.24
17_L	125_F	1.056	0.24
71_G	243_S	1.052	0.24
95_L	125_F	1.052	0.24
28_T	103_F	1.044	0.24
174_I	255_F	1.038	0.24
164_I	171_I	1.037	0.24
34_R	105_A	1.035	0.24
82_F	178_S	1.017	0.23
66_L	81_Q	1.016	0.23
161_L	251_A	1.016	0.23
92_G	219_L	1.012	0.23
11_I	14_F	1.006	0.23
161_L	215_K	1.002	0.23
169_T	173_T	0.998	0.23
49_V	53_R	0.993	0.22
80_E	163_V	0.992	0.22
93_T	169_T	0.990	0.22
64_G	86_I	0.987	0.22
27_A	37_F	0.983	0.22
51_V	87_F	0.979	0.22
171_I	174_I	0.978	0.22
70_A	111_I	0.974	0.22
116_G	152_F	0.972	0.22
86_I	130_S	0.971	0.22
95_L	207_L	0.968	0.22
83_R	90_T	0.964	0.22
93_T	204_A	0.963	0.22
48_M	57_M	0.963	0.22
191_T	244_R	0.955	0.21
160_R	200_I	0.947	0.21
68_D	172_Y	0.946	0.21
115_A	217_S	0.944	0.21
16_L	170_S	0.944	0.21
51_V	80_E	0.943	0.21
22_E	25_A	0.941	0.21
206_M	213_D	0.939	0.21
26_Y	144_P	0.938	0.21
53_R	205_T	0.934	0.21
83_R	103_F	0.934	0.21
189_R	255_F	0.931	0.21
37_F	218_V	0.930	0.21
161_L	184_L	0.926	0.20
13_C	95_L	0.923	0.20
12_F	62_F	0.919	0.20
242_T	249_L	0.918	0.20
152_F	163_V	0.915	0.20
86_I	89_S	0.914	0.20
40_S	156_L	0.912	0.20
173_T	204_A	0.908	0.20
180_L	251_A	0.905	0.20
62_F	192_T	0.905	0.20
21_I	46_N	0.902	0.20
155_R	238_V	0.896	0.20
35_V	63_T	0.893	0.20
57_M	198_G	0.892	0.20
21_I	110_A	0.887	0.19
7_Q	92_G	0.885	0.19
248_T	259_A	0.884	0.19
115_A	129_F	0.883	0.19
176_V	252_Q	0.882	0.19
183_G	235_W	0.878	0.19
88_G	256_I	0.875	0.19
14_F	58_V	0.874	0.19
223_V	233_L	0.868	0.19
174_I	178_S	0.867	0.19
157_I	207_L	0.850	0.18
13_C	140_Y	0.849	0.18
35_V	266_T	0.848	0.18
88_G	259_A	0.845	0.18
162_F	220_A	0.845	0.18
28_T	107_F	0.840	0.18
100_L	129_F	0.837	0.18
64_G	158_P	0.810	0.17
58_V	104_V	0.806	0.17
22_E	119_G	0.801	0.17
115_A	240_M	0.801	0.17
230_Y	234_K	0.798	0.17
24_L	197_S	0.798	0.17
27_A	139_S	0.792	0.17
259_A	263_A	0.791	0.17
153_H	217_S	0.790	0.17
197_S	204_A	0.784	0.17
28_T	246_A	0.780	0.17
175_G	194_V	0.776	0.17
182_A	187_P	0.774	0.17
141_L	167_L	0.773	0.17
78_V	199_L	0.772	0.16
14_F	102_S	0.772	0.16
9_L	27_A	0.770	0.16
30_L	64_G	0.769	0.16
86_I	157_I	0.768	0.16
89_S	254_M	0.766	0.16
77_I	253_L	0.761	0.16
90_T	250_L	0.761	0.16
145_S	183_G	0.760	0.16
11_I	58_V	0.759	0.16
107_F	121_V	0.756	0.16
68_D	266_T	0.753	0.16
17_L	249_L	0.753	0.16
59_Q	173_T	0.744	0.16
43_S	212_V	0.743	0.16
193_A	221_D	0.742	0.16
185_L	259_A	0.738	0.16
13_C	227_K	0.731	0.16
27_A	238_V	0.729	0.15
22_E	217_S	0.728	0.15
164_I	200_I	0.726	0.15
102_S	144_P	0.722	0.15
18_I	24_L	0.720	0.15
23_T	103_F	0.718	0.15
104_V	145_S	0.718	0.15
212_V	216_V	0.715	0.15
143_L	253_L	0.713	0.15
28_T	158_P	0.710	0.15
20_S	114_L	0.710	0.15
176_V	179_A	0.709	0.15
130_S	170_S	0.709	0.15
36_G	146_I	0.708	0.15
51_V	72_K	0.708	0.15
69_D	188_E	0.707	0.15
123_Q	131_K	0.704	0.15
78_V	246_A	0.702	0.15
52_S	61_P	0.702	0.15
64_G	179_A	0.696	0.15
161_L	192_T	0.694	0.15
28_T	49_V	0.691	0.15
9_L	28_T	0.687	0.15
184_L	212_V	0.683	0.14
56_N	176_V	0.679	0.14
94_I	258_G	0.679	0.14
111_I	148_Y	0.676	0.14
170_S	243_S	0.676	0.14
245_V	249_L	0.673	0.14
85_L	217_S	0.669	0.14
236_T	244_R	0.665	0.14
83_R	255_F	0.662	0.14
95_L	139_S	0.662	0.14
55_S	224_A	0.660	0.14
19_H	89_S	0.657	0.14
56_N	250_L	0.654	0.14
82_F	223_V	0.651	0.14
34_R	113_H	0.650	0.14
201_N	204_A	0.649	0.14
86_I	240_M	0.648	0.14
95_L	131_K	0.647	0.14
146_I	150_K	0.646	0.14
90_T	252_Q	0.646	0.14
37_F	235_W	0.644	0.14
48_M	62_F	0.640	0.14
9_L	146_I	0.638	0.14
41_A	104_V	0.638	0.14
132_Q	183_G	0.636	0.13
133_G	212_V	0.635	0.13
149_V	163_V	0.635	0.13
164_I	207_L	0.631	0.13
88_G	138_L	0.631	0.13
175_G	208_L	0.629	0.13
51_V	95_L	0.628	0.13
53_R	206_M	0.628	0.13
43_S	92_G	0.627	0.13
125_F	229_S	0.627	0.13
97_I	102_S	0.623	0.13
161_L	212_V	0.623	0.13
41_A	225_K	0.622	0.13
24_L	204_A	0.621	0.13
12_F	88_G	0.618	0.13
94_I	170_S	0.618	0.13
59_Q	158_P	0.617	0.13
11_I	32_G	0.616	0.13
243_S	264_W	0.615	0.13
141_L	194_V	0.615	0.13
47_V	138_L	0.615	0.13
115_A	236_T	0.614	0.13
63_T	190_S	0.614	0.13
85_L	233_L	0.609	0.13
102_S	187_P	0.609	0.13
110_A	157_I	0.608	0.13
123_Q	245_V	0.607	0.13
25_A	218_V	0.605	0.13
67_I	87_F	0.599	0.13
14_F	54_M	0.597	0.13
90_T	176_V	0.596	0.13
176_V	249_L	0.596	0.13
85_L	242_T	0.594	0.13
50_I	174_I	0.592	0.13
9_L	95_L	0.588	0.13
89_S	179_A	0.588	0.13
121_V	209_A	0.586	0.12
22_E	111_I	0.585	0.12
129_F	139_S	0.585	0.12
202_G	205_T	0.583	0.12
10_F	123_Q	0.582	0.12
219_L	222_D	0.582	0.12
161_L	243_S	0.582	0.12
65_H	136_N	0.578	0.12
52_S	263_A	0.577	0.12
150_K	265_L	0.576	0.12
79_G	200_I	0.575	0.12
98_I	125_F	0.575	0.12
96_G	110_A	0.575	0.12
87_F	254_M	0.575	0.12
8_V	123_Q	0.573	0.12
160_R	224_A	0.573	0.12
192_T	266_T	0.572	0.12
160_R	196_A	0.572	0.12
247_G	257_P	0.571	0.12
37_F	47_V	0.570	0.12
43_S	115_A	0.568	0.12
194_V	234_K	0.567	0.12
17_L	151_G	0.567	0.12
11_I	66_L	0.566	0.12
24_L	205_T	0.562	0.12
50_I	220_A	0.561	0.12
11_I	191_T	0.560	0.12
189_R	192_T	0.559	0.12
78_V	184_L	0.558	0.12
84_F	124_V	0.557	0.12
15_L	252_Q	0.557	0.12
35_V	265_L	0.557	0.12
43_S	131_K	0.554	0.12
36_G	229_S	0.554	0.12
147_S	254_M	0.553	0.12
163_V	166_M	0.552	0.12
132_Q	145_S	0.547	0.12
16_L	92_G	0.547	0.12
122_F	125_F	0.546	0.12
60_Q	220_A	0.546	0.12
64_G	161_L	0.544	0.12
43_S	216_V	0.543	0.12
219_L	223_V	0.540	0.12
168_I	203_I	0.539	0.12
68_D	190_S	0.538	0.12
98_I	203_I	0.538	0.12
91_V	185_L	0.537	0.12
172_Y	198_G	0.536	0.12
168_I	223_V	0.536	0.12
83_R	88_G	0.535	0.12
32_G	38_I	0.533	0.12
19_H	48_M	0.532	0.12
178_S	182_A	0.531	0.11
243_S	267_K	0.528	0.11
36_G	154_M	0.527	0.11
180_L	252_Q	0.526	0.11
101_P	165_N	0.523	0.11
43_S	177_L	0.521	0.11
9_L	160_R	0.519	0.11
21_I	61_P	0.517	0.11
38_I	41_A	0.517	0.11
95_L	179_A	0.516	0.11
120_S	165_N	0.512	0.11
24_L	51_V	0.509	0.11
189_R	203_I	0.509	0.11
25_A	222_D	0.506	0.11
46_N	100_L	0.506	0.11
56_N	244_R	0.506	0.11
104_V	172_Y	0.505	0.11
163_V	212_V	0.505	0.11
67_I	95_L	0.504	0.11
41_A	63_T	0.504	0.11
176_V	244_R	0.504	0.11
55_S	189_R	0.502	0.11
28_T	218_V	0.502	0.11
85_L	206_M	0.500	0.11

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
4akfA	2	0.4944	6.9	0.977	Contact Map
4jifB	1	0.0706	5.5	0.978	Contact Map
3wdoA	1	0.8401	4.7	0.978	Contact Map
3w4tA	1	0.9257	4.6	0.978	Contact Map
1pw4A	1	0.8253	4.6	0.978	Contact Map
2cfqA	1	0.8476	3.3	0.98	Contact Map
4lz6A	1	0.4461	2.5	0.981	Contact Map
1irzA	1	0.2305	2.1	0.982	Contact Map
3mktA	1	0.4424	2	0.982	Contact Map
3klyA	3	0.4312	2	0.982	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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