YVCA - BACSU - GREMLIN Contacts

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YVCA - Putative lipoprotein YvcA

UniProt:	O06965	Sequences: MKKIIFICFSLLLALTGGCSMNDNDKNSTNDNKTEAVKPKDMDPKDLPQVPAFQDEKTREYMVSTKEEEPGYYLLESKLKGFRMLFPEDGKYLSRRSSLTGKNKESIGFNSYDKDTNVMFDGHVTYYKEESFANEPKTMLDIVSGKNDYKGEYKKSSKKKTDIYTAKKKDIFDDIDRKYNYSYSYFGYVKSTEEDNLGVEYAFTLGCKNENQPCSLDEEKAKNKVEKLINSITFLIDKKEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	241 (203)
Sequences:	129 (97)
Seq/√Len:	6.8

BACSU - YVCA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
207_C	214_C	3.897	0.95
48_P	53_F	3.123	0.85
62_M	78_K	2.959	0.82
79_L	97_S	2.882	0.80
69_E	85_L	2.756	0.77
61_Y	75_L	2.687	0.75
53_F	62_M	2.629	0.73
17_G	21_M	2.574	0.71
153_Y	186_F	2.491	0.69
156_S	220_K	2.439	0.67
63_V	74_L	2.433	0.67
59_R	73_Y	2.430	0.67
79_L	82_F	2.300	0.62
5_I	10_S	2.275	0.61
116_T	188_Y	2.265	0.61
57_K	75_L	2.126	0.56
49_Q	61_Y	2.102	0.55
12_L	15_L	2.073	0.54
64_S	73_Y	2.025	0.52
164_Y	231_S	2.017	0.52
69_E	76_E	1.974	0.50
5_I	15_L	1.860	0.46
53_F	117_N	1.858	0.46
50_V	85_L	1.825	0.44
167_K	222_K	1.809	0.44
53_F	188_Y	1.782	0.43
163_I	195_D	1.744	0.41
8_C	12_L	1.706	0.40
206_G	210_E	1.691	0.39
57_K	61_Y	1.686	0.39
153_Y	210_E	1.671	0.39
48_P	59_R	1.653	0.38
48_P	73_Y	1.631	0.37
186_F	228_L	1.600	0.36
166_A	232_I	1.543	0.34
7_I	15_L	1.516	0.33
5_I	8_C	1.505	0.33
48_P	64_S	1.500	0.33
189_V	232_I	1.494	0.33
12_L	23_D	1.493	0.33
77_S	234_F	1.459	0.31
11_L	15_L	1.450	0.31
69_E	227_K	1.449	0.31
76_E	85_L	1.439	0.31
101_G	226_E	1.430	0.31
16_T	20_S	1.429	0.30
156_S	178_K	1.409	0.30
216_L	221_A	1.406	0.30
47_L	60_E	1.386	0.29
225_V	229_I	1.367	0.29
8_C	13_L	1.364	0.28
78_K	83_R	1.347	0.28
106_S	199_V	1.341	0.28
144_S	153_Y	1.338	0.28
53_F	59_R	1.331	0.27
64_S	90_G	1.316	0.27
81_G	151_G	1.313	0.27
96_R	121_D	1.307	0.27
68_E	74_L	1.304	0.27
53_F	73_Y	1.304	0.27
187_G	229_I	1.296	0.26
73_Y	188_Y	1.281	0.26
8_C	23_D	1.274	0.26
63_V	82_F	1.272	0.26
48_P	66_K	1.271	0.26
7_I	10_S	1.258	0.25
68_E	225_V	1.250	0.25
13_L	21_M	1.248	0.25
11_L	22_N	1.229	0.24
159_K	180_N	1.218	0.24
159_K	223_N	1.205	0.24
45_K	57_K	1.204	0.24
47_L	65_T	1.199	0.24
126_Y	191_S	1.198	0.24
162_D	230_N	1.191	0.23
162_D	192_T	1.186	0.23
140_L	214_C	1.176	0.23
81_G	191_S	1.174	0.23
140_L	207_C	1.173	0.23
133_A	142_I	1.170	0.23
140_L	149_Y	1.165	0.23
59_R	66_K	1.164	0.23
165_T	226_E	1.162	0.23
15_L	18_G	1.160	0.23
19_C	64_S	1.157	0.22
58_T	189_V	1.144	0.22
82_F	97_S	1.144	0.22
56_E	65_T	1.142	0.22
94_S	205_L	1.140	0.22
50_V	53_F	1.100	0.21
5_I	12_L	1.093	0.21
87_P	214_C	1.092	0.21
58_T	61_Y	1.088	0.21
6_F	12_L	1.080	0.21
50_V	59_R	1.078	0.20
189_V	210_E	1.078	0.20
77_S	86_F	1.076	0.20
163_I	199_V	1.062	0.20
86_F	231_S	1.056	0.20
49_Q	109_F	1.048	0.20
157_S	220_K	1.035	0.19
51_P	88_E	1.021	0.19
97_S	234_F	1.018	0.19
72_Y	110_N	1.017	0.19
47_L	64_S	1.013	0.19
189_V	225_V	1.012	0.19
225_V	228_L	1.012	0.19
75_L	79_L	1.005	0.19
176_D	192_T	1.002	0.19
47_L	59_R	1.002	0.19
57_K	92_Y	0.999	0.19
131_S	230_N	0.996	0.19
142_I	199_V	0.995	0.19
84_M	87_P	0.995	0.19
209_N	221_A	0.991	0.18
16_T	23_D	0.986	0.18
54_Q	63_V	0.969	0.18
112_Y	185_Y	0.968	0.18
74_L	187_G	0.968	0.18
62_M	144_S	0.963	0.18
13_L	16_T	0.943	0.17
61_Y	200_E	0.937	0.17
187_G	225_V	0.936	0.17
195_D	199_V	0.935	0.17
141_D	187_G	0.933	0.17
109_F	161_T	0.931	0.17
50_V	79_L	0.926	0.17
91_K	109_F	0.924	0.17
86_F	228_L	0.919	0.17
5_I	11_L	0.917	0.17
47_L	50_V	0.913	0.17
189_V	196_N	0.910	0.17
80_K	211_N	0.906	0.17
197_L	201_Y	0.905	0.17
149_Y	166_A	0.902	0.16
10_S	15_L	0.901	0.16
70_P	79_L	0.898	0.16
59_R	63_V	0.895	0.16
67_E	190_K	0.889	0.16
144_S	183_Y	0.888	0.16
82_F	181_Y	0.887	0.16
15_L	20_S	0.882	0.16
153_Y	228_L	0.867	0.16
217_D	220_K	0.866	0.16
135_E	150_K	0.857	0.16
99_L	185_Y	0.856	0.16
140_L	164_Y	0.847	0.15
15_L	22_N	0.847	0.15
11_L	20_S	0.840	0.15
94_S	124_V	0.840	0.15
10_S	24_N	0.835	0.15
76_E	83_R	0.834	0.15
7_I	22_N	0.833	0.15
63_V	83_R	0.831	0.15
88_E	199_V	0.823	0.15
58_T	75_L	0.819	0.15
189_V	201_Y	0.819	0.15
6_F	13_L	0.818	0.15
90_G	191_S	0.813	0.15
11_L	21_M	0.806	0.15
23_D	61_Y	0.802	0.14
108_G	211_N	0.802	0.14
56_E	71_G	0.799	0.14
59_R	64_S	0.796	0.14
14_A	80_K	0.796	0.14
187_G	201_Y	0.793	0.14
101_G	153_Y	0.788	0.14
22_N	73_Y	0.786	0.14
55_D	58_T	0.785	0.14
83_R	197_L	0.781	0.14
133_A	153_Y	0.781	0.14
88_E	106_S	0.775	0.14
7_I	11_L	0.775	0.14
201_Y	212_Q	0.773	0.14
200_E	232_I	0.766	0.14
165_T	199_V	0.759	0.14
57_K	105_E	0.753	0.14
60_E	78_K	0.751	0.14
6_F	9_F	0.748	0.14
10_S	19_C	0.744	0.13
104_K	130_E	0.739	0.13
157_S	211_N	0.737	0.13
54_Q	82_F	0.733	0.13
107_I	149_Y	0.727	0.13
157_S	227_K	0.721	0.13
70_P	189_V	0.721	0.13
109_F	184_S	0.717	0.13
145_G	200_E	0.715	0.13
131_S	135_E	0.711	0.13
148_D	185_Y	0.710	0.13
140_L	231_S	0.710	0.13
90_G	144_S	0.707	0.13
48_P	71_G	0.707	0.13
14_A	20_S	0.701	0.13
12_L	16_T	0.700	0.13
72_Y	169_K	0.699	0.13
82_F	136_P	0.698	0.13
12_L	68_E	0.696	0.13
10_S	20_S	0.696	0.13
11_L	19_C	0.694	0.13
49_Q	126_Y	0.691	0.13
152_E	223_N	0.686	0.12
115_D	209_N	0.685	0.12
19_C	56_E	0.684	0.12
72_Y	224_K	0.684	0.12
53_F	70_P	0.680	0.12
50_V	74_L	0.680	0.12
50_V	73_Y	0.674	0.12
108_G	120_F	0.673	0.12
88_E	104_K	0.668	0.12
74_L	85_L	0.658	0.12
121_D	138_T	0.657	0.12
49_Q	82_F	0.654	0.12
13_L	23_D	0.654	0.12
52_A	234_F	0.654	0.12
90_G	183_Y	0.651	0.12
61_Y	72_Y	0.646	0.12
10_S	13_L	0.646	0.12
19_C	90_G	0.646	0.12
82_F	234_F	0.645	0.12
138_T	145_G	0.644	0.12
9_F	13_L	0.642	0.12
69_E	151_G	0.637	0.12
58_T	84_M	0.636	0.12
5_I	13_L	0.635	0.12
49_Q	75_L	0.635	0.12
7_I	20_S	0.635	0.12
67_E	72_Y	0.634	0.12
54_Q	74_L	0.633	0.12
122_G	232_I	0.633	0.12
126_Y	232_I	0.631	0.12
219_E	223_N	0.626	0.11
133_A	149_Y	0.623	0.11
51_P	59_R	0.617	0.11
66_K	223_N	0.617	0.11
60_E	83_R	0.612	0.11
89_D	117_N	0.607	0.11
54_Q	79_L	0.606	0.11
69_E	81_G	0.606	0.11
11_L	16_T	0.605	0.11
123_H	152_E	0.602	0.11
135_E	189_V	0.599	0.11
188_Y	201_Y	0.597	0.11
155_K	212_Q	0.596	0.11
99_L	222_K	0.592	0.11
212_Q	232_I	0.588	0.11
87_P	207_C	0.587	0.11
62_M	190_K	0.587	0.11
47_L	54_Q	0.586	0.11
189_V	212_Q	0.585	0.11
62_M	188_Y	0.584	0.11
61_Y	105_E	0.583	0.11
8_C	61_Y	0.582	0.11
123_H	156_S	0.582	0.11
155_K	164_Y	0.580	0.11
62_M	84_M	0.579	0.11
72_Y	198_G	0.573	0.11
100_T	200_E	0.571	0.11
24_N	82_F	0.569	0.11
108_G	157_S	0.569	0.11
55_D	84_M	0.567	0.11
93_L	161_T	0.565	0.11
117_N	186_F	0.565	0.11
114_K	204_T	0.565	0.11
20_S	83_R	0.564	0.11
164_Y	188_Y	0.559	0.11
149_Y	207_C	0.556	0.10
63_V	69_E	0.553	0.10
46_D	50_V	0.553	0.10
67_E	81_G	0.552	0.10
63_V	85_L	0.550	0.10
71_G	148_D	0.549	0.10
183_Y	189_V	0.549	0.10
226_E	230_N	0.542	0.10
46_D	54_Q	0.540	0.10
90_G	201_Y	0.538	0.10
87_P	105_E	0.536	0.10
195_D	198_G	0.536	0.10
98_S	116_T	0.535	0.10
16_T	19_C	0.534	0.10
64_S	198_G	0.533	0.10
45_K	107_I	0.530	0.10
9_F	17_G	0.530	0.10
123_H	211_N	0.529	0.10
11_L	23_D	0.527	0.10
171_I	229_I	0.526	0.10
88_E	209_N	0.522	0.10
72_Y	166_A	0.522	0.10
9_F	24_N	0.519	0.10
56_E	151_G	0.518	0.10
178_K	218_E	0.515	0.10
57_K	79_L	0.514	0.10
68_E	218_E	0.514	0.10
212_Q	222_K	0.511	0.10
5_I	199_V	0.510	0.10
155_K	234_F	0.510	0.10
63_V	141_D	0.510	0.10
52_A	71_G	0.509	0.10
6_F	11_L	0.508	0.10
17_G	24_N	0.505	0.10
54_Q	64_S	0.504	0.10
165_T	217_D	0.502	0.10
19_C	54_Q	0.501	0.10
57_K	122_G	0.500	0.10

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
3zbiC	1	0.1162	53	0.954	Contact Map
4jg9A	2	0.5768	44	0.956	Contact Map
4v33A	1	0.7012	10.5	0.968	Contact Map
4i0uA	4	0.1992	7.9	0.969	Contact Map
4ev6A	3	0.2075	7.1	0.97	Contact Map
2z14A	2	0.278	6.6	0.97	Contact Map
2lzrA	1	0.1867	6	0.971	Contact Map
4apwA	6	0.2282	4.6	0.973	Contact Map
4pj0U	1	0.3527	3.6	0.974	Contact Map
2zxeG	1	0.0747	3.6	0.974	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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