YBBA - BACSU - GREMLIN Contacts

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YBBA - Uncharacterized protein YbbA

UniProt:	P55192	Sequences: MKGSLSEHKAGNRRFTLYLPPSYSTDSGGFPAVYVQDGSSLFQNQIELLESAFQQQRLPELVLIGIEPENRLDEYTPWPAASLSDRFTDFGGMGYHYLSDITNQFIPLIEENWNVTREPQSRGMIGASLGGLISMFAILKYPSMFGKIGSISGSYWYENAAETIHISSLKPGTARVFMSIGSEEGREKQSIQRHMLKKTKQVHQSLKEKGFTEDQLCLSIEKGAVHHHKYFCKQFINALEWLYGKNRSTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	250 (215)
Sequences:	9628 (7146)
Seq/√Len:	487.3

ECOLI - FES SFGH1 SFGH2 YIEL
BACSU - YBBA BESA YJCH
SULSO - Q97UM5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
138_I	148_I	4.103	1.00
110_E	122_R	3.593	1.00
108_L	112_N	3.005	1.00
116_T	121_S	2.968	1.00
203_H	207_K	2.817	1.00
150_S	153_G	2.801	1.00
182_S	222_K	2.583	1.00
219_S	237_N	2.541	1.00
99_S	103_N	2.511	1.00
205_S	209_K	2.405	1.00
110_E	115_V	2.327	1.00
33_V	61_L	2.324	1.00
62_V	115_V	2.321	1.00
151_I	238_A	2.281	1.00
196_L	200_K	2.241	1.00
23_Y	114_N	2.235	1.00
98_L	141_Y	2.211	1.00
22_S	60_E	2.211	1.00
200_K	220_I	2.157	1.00
149_G	238_A	2.121	1.00
123_G	147_K	2.035	1.00
32_A	64_I	2.028	1.00
34_Y	122_R	1.938	1.00
98_L	137_A	1.928	1.00
179_S	234_Q	1.897	1.00
106_I	122_R	1.878	1.00
33_V	125_I	1.877	1.00
30_F	62_V	1.849	1.00
64_I	109_I	1.840	1.00
19_L	62_V	1.816	1.00
17_L	64_I	1.775	1.00
35_V	125_I	1.746	1.00
34_Y	106_I	1.713	1.00
203_H	213_E	1.646	1.00
109_I	115_V	1.609	1.00
98_L	140_K	1.574	1.00
23_Y	30_F	1.526	1.00
118_E	121_S	1.523	1.00
148_I	176_V	1.516	1.00
204_Q	208_E	1.485	1.00
28_G	60_E	1.476	1.00
34_Y	110_E	1.474	1.00
100_D	105_F	1.470	1.00
204_Q	207_K	1.447	1.00
15_F	105_F	1.418	1.00
102_T	141_Y	1.408	1.00
177_F	219_S	1.403	1.00
110_E	117_R	1.394	1.00
182_S	220_I	1.392	1.00
153_G	199_T	1.391	1.00
57_R	240_E	1.368	1.00
134_S	148_I	1.363	1.00
125_I	149_G	1.362	1.00
236_I	240_E	1.356	1.00
127_A	231_F	1.350	1.00
36_Q	133_I	1.348	1.00
135_M	150_S	1.338	1.00
200_K	204_Q	1.331	1.00
203_H	218_L	1.309	1.00
147_K	175_R	1.306	1.00
15_F	108_L	1.299	1.00
201_Q	204_Q	1.291	1.00
136_F	140_K	1.289	1.00
135_M	155_Y	1.287	1.00
36_Q	97_Y	1.284	1.00
103_N	107_P	1.283	1.00
165_H	168_S	1.270	1.00
213_E	218_L	1.265	1.00
30_F	114_N	1.256	1.00
106_I	144_M	1.255	1.00
71_R	74_E	1.241	1.00
162_E	165_H	1.241	1.00
103_N	141_Y	1.238	1.00
59_P	239_L	1.217	1.00
131_G	150_S	1.216	1.00
36_Q	124_M	1.209	1.00
124_M	134_S	1.183	1.00
107_P	144_M	1.178	1.00
205_S	208_E	1.170	1.00
18_Y	50_E	1.170	1.00
6_S	104_Q	1.166	1.00
32_A	115_V	1.149	1.00
124_M	148_I	1.130	1.00
203_H	220_I	1.129	1.00
35_V	46_I	1.127	1.00
106_I	145_F	1.124	1.00
33_V	63_L	1.115	1.00
102_T	144_M	1.112	1.00
29_G	114_N	1.112	1.00
164_I	167_S	1.110	1.00
47_E	51_S	1.108	1.00
197_K	201_Q	1.103	1.00
141_Y	144_M	1.101	1.00
98_L	102_T	1.099	1.00
125_I	151_I	1.096	1.00
162_E	167_S	1.082	1.00
128_S	226_H	1.066	1.00
14_R	43_Q	1.063	1.00
207_K	213_E	1.060	1.00
75_Y	78_W	1.057	1.00
164_I	168_S	1.033	1.00
49_L	63_L	1.027	1.00
122_R	144_M	1.026	1.00
34_Y	64_I	1.025	1.00
155_Y	202_V	1.024	1.00
37_D	41_L	1.024	1.00
124_M	137_A	1.022	1.00
13_R	100_D	1.021	1.00
8_H	104_Q	1.019	1.00
6_S	9_K	1.015	1.00
34_Y	109_I	1.014	1.00
149_G	242_L	1.012	1.00
8_H	99_S	1.011	1.00
134_S	150_S	1.006	1.00
199_T	218_L	1.005	1.00
29_G	116_T	1.004	1.00
62_V	113_W	1.004	1.00
51_S	55_Q	1.001	1.00
24_S	27_S	0.998	1.00
19_L	23_Y	0.996	1.00
175_R	241_W	0.986	1.00
178_M	203_H	0.967	1.00
152_S	231_F	0.957	1.00
32_A	122_R	0.954	1.00
14_R	67_E	0.952	1.00
178_M	199_T	0.951	1.00
221_E	234_Q	0.951	1.00
206_L	211_F	0.948	1.00
35_V	65_G	0.945	1.00
31_P	61_L	0.941	1.00
100_D	104_Q	0.936	1.00
9_K	13_R	0.934	1.00
206_L	213_E	0.931	1.00
15_F	100_D	0.928	1.00
156_W	201_Q	0.927	1.00
180_I	195_M	0.925	1.00
25_T	114_N	0.924	1.00
51_S	54_Q	0.922	1.00
74_E	77_P	0.910	1.00
22_S	30_F	0.910	1.00
101_I	137_A	0.900	1.00
106_I	110_E	0.900	1.00
64_I	105_F	0.893	1.00
217_C	241_W	0.886	1.00
59_P	240_E	0.881	1.00
152_S	184_E	0.881	1.00
24_S	114_N	0.872	1.00
73_D	78_W	0.871	1.00
71_R	75_Y	0.870	1.00
163_T	166_I	0.865	1.00
202_V	206_L	0.865	1.00
77_P	99_S	0.865	1.00
182_S	223_G	0.863	1.00
36_Q	66_I	0.862	1.00
182_S	221_E	0.862	1.00
106_I	109_I	0.861	1.00
34_Y	145_F	0.857	1.00
102_T	137_A	0.856	1.00
237_N	240_E	0.848	1.00
108_L	111_E	0.840	1.00
150_S	178_M	0.840	1.00
58_L	61_L	0.828	1.00
55_Q	236_I	0.827	1.00
135_M	176_V	0.824	1.00
127_A	228_H	0.811	1.00
55_Q	59_P	0.809	1.00
37_D	42_F	0.808	1.00
156_W	159_N	0.806	1.00
151_I	231_F	0.800	1.00
179_S	230_Y	0.799	1.00
181_G	223_G	0.794	1.00
30_F	60_E	0.791	1.00
135_M	153_G	0.785	1.00
121_S	146_G	0.778	1.00
7_E	10_A	0.774	1.00
196_L	220_I	0.773	1.00
17_L	62_V	0.766	1.00
234_Q	237_N	0.766	1.00
74_E	78_W	0.765	1.00
138_I	174_A	0.759	1.00
132_L	136_F	0.755	1.00
152_S	181_G	0.752	1.00
8_H	103_N	0.752	1.00
103_N	144_M	0.752	1.00
18_Y	53_F	0.748	1.00
179_S	221_E	0.747	1.00
221_E	230_Y	0.744	1.00
96_H	99_S	0.743	1.00
50_E	53_F	0.741	1.00
102_T	107_P	0.741	1.00
73_D	77_P	0.741	1.00
221_E	237_N	0.739	1.00
16_T	43_Q	0.736	1.00
24_S	29_G	0.736	1.00
61_L	243_Y	0.735	1.00
110_E	144_M	0.733	1.00
123_G	243_Y	0.733	1.00
224_A	230_Y	0.732	1.00
230_Y	234_Q	0.731	1.00
151_I	179_S	0.731	1.00
160_A	198_K	0.722	1.00
183_E	223_G	0.721	1.00
55_Q	58_L	0.720	1.00
195_M	198_K	0.718	1.00
123_G	146_G	0.716	1.00
66_I	101_I	0.716	1.00
32_A	63_L	0.714	1.00
19_L	113_W	0.700	1.00
162_E	166_I	0.696	1.00
197_K	200_K	0.689	1.00
35_V	235_F	0.687	1.00
198_K	201_Q	0.686	1.00
151_I	234_Q	0.685	1.00
56_Q	59_P	0.683	1.00
123_G	149_G	0.683	1.00
31_P	60_E	0.682	1.00
45_Q	228_H	0.677	1.00
19_L	30_F	0.676	1.00
107_P	145_F	0.674	1.00
130_G	133_I	0.672	1.00
116_T	122_R	0.670	1.00
227_H	230_Y	0.667	1.00
180_I	199_T	0.666	1.00
32_A	62_V	0.666	1.00
147_K	242_L	0.665	1.00
102_T	145_F	0.659	1.00
16_T	67_E	0.659	1.00
175_R	212_T	0.655	1.00
37_D	66_I	0.655	1.00
183_E	222_K	0.654	1.00
200_K	218_L	0.653	1.00
32_A	110_E	0.647	1.00
131_G	153_G	0.647	1.00
23_Y	29_G	0.644	1.00
17_L	113_W	0.644	1.00
41_L	45_Q	0.643	1.00
97_Y	133_I	0.642	1.00
37_D	45_Q	0.642	1.00
16_T	44_N	0.640	1.00
51_S	236_I	0.639	1.00
102_T	106_I	0.639	1.00
98_L	136_F	0.634	1.00
132_L	154_S	0.634	1.00
169_L	172_G	0.632	1.00
170_K	173_T	0.631	1.00
53_F	56_Q	0.629	1.00
180_I	218_L	0.626	1.00
163_T	167_S	0.625	1.00
235_F	239_L	0.623	1.00
94_G	133_I	0.618	0.99
174_A	211_F	0.614	0.99
75_Y	79_P	0.612	0.99
31_P	121_S	0.611	0.99
54_Q	58_L	0.609	0.99
48_L	53_F	0.608	0.99
135_M	202_V	0.608	0.99
27_S	114_N	0.607	0.99
171_P	174_A	0.604	0.99
221_E	233_K	0.603	0.99
147_K	241_W	0.599	0.99
25_T	30_F	0.599	0.99
42_F	65_G	0.598	0.99
24_S	28_G	0.592	0.99
122_R	146_G	0.591	0.99
201_Q	205_S	0.585	0.99
195_M	199_T	0.584	0.99
124_M	145_F	0.583	0.99
53_F	58_L	0.582	0.99
7_E	104_Q	0.580	0.99
31_P	116_T	0.578	0.99
8_H	96_H	0.577	0.99
23_Y	62_V	0.575	0.99
172_G	211_F	0.575	0.99
49_L	53_F	0.574	0.99
178_M	213_E	0.574	0.99
52_A	56_Q	0.572	0.99
29_G	117_R	0.572	0.99
107_P	111_E	0.569	0.99
77_P	80_A	0.566	0.99
179_S	219_S	0.564	0.99
53_F	60_E	0.564	0.99
37_D	40_S	0.564	0.99
181_G	184_E	0.560	0.99
105_F	109_I	0.560	0.99
233_K	236_I	0.559	0.99
47_E	50_E	0.557	0.99
229_K	233_K	0.556	0.99
25_T	29_G	0.555	0.99
138_I	142_P	0.554	0.99
127_A	153_G	0.548	0.99
36_Q	127_A	0.547	0.99
69_E	72_L	0.547	0.99
13_R	68_P	0.546	0.99
180_I	196_L	0.546	0.99
105_F	108_L	0.546	0.99
207_K	210_G	0.543	0.99
38_G	128_S	0.533	0.99
213_E	217_C	0.533	0.99
178_M	206_L	0.532	0.98
125_I	235_F	0.532	0.98
107_P	110_E	0.528	0.98
36_Q	134_S	0.528	0.98
13_R	105_F	0.525	0.98
178_M	202_V	0.522	0.98
62_V	114_N	0.518	0.98
129_L	133_I	0.518	0.98
44_N	48_L	0.516	0.98
48_L	51_S	0.516	0.98
56_Q	60_E	0.516	0.98
150_S	176_V	0.514	0.98
17_L	32_A	0.511	0.98
23_Y	113_W	0.511	0.98
18_Y	63_L	0.511	0.98
170_K	174_A	0.509	0.98
135_M	178_M	0.508	0.98
43_Q	67_E	0.507	0.98
62_V	109_I	0.506	0.98
23_Y	115_V	0.504	0.98
76_T	79_P	0.504	0.98
110_E	116_T	0.504	0.98
33_V	239_L	0.502	0.98
200_K	203_H	0.500	0.98

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
4w9rA	2	0.916	100	0.371	Contact Map
3gffA	2	0.972	100	0.409	Contact Map
1jjfA	1	0.888	100	0.423	Contact Map
3c8dA	2	0.872	100	0.434	Contact Map
3ls2A	2	0.92	100	0.437	Contact Map
2gzsA	1	0.88	100	0.442	Contact Map
2uz0A	4	0.86	100	0.447	Contact Map
4rotA	4	0.884	100	0.452	Contact Map
3i6yA	1	0.924	100	0.458	Contact Map
3e4dA	3	0.924	100	0.467	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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