YIGB - ECOLI - GREMLIN Contacts

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YIGB - Flavin mononucleotide phosphatase YigB

UniProt:	P0ADP0	Sequences: MRFYRPLGRISALTFDLDDTLYDNRPVILRTEREALTFVQNYHPALRSFQNEDLQRLRQAVREAEPEIYHDVTRWRFRSIEQAMLDAGLSAEEASAGAHAAMINFAKWRSRIDVPQQTHDTLKQLAKKWPLVAITNGNAQPELFGLGDYFEFVLRAGPHGRSKPFSDMYFLAAEKLNVPIGEILHVGDDLTTDVGGAIRSGMQACWIRPENGDLMQTWDSRLLPHLEISRLASLTSLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11202
Length:	238 (200)
Sequences:	26232 (20853)
Seq/√Len:	1474.5

ECOLI - YIGB GPH YRFG YIEH YNIC YJJG YFBT PGMB YQAB YIHX
BACSU - YSAA YFNB YHCW PPAX PGMB
HALSA - Q9HQE2 Q9HP74 Q9HSS2 Q9HMC4
SULSO - Q7LXL6 Q7LX46 Q97ZU6 Q97WT6 Q97YZ1 Q97X58

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_S	182_E	4.263	1.00
171_L	175_K	2.957	1.00
142_E	147_G	2.847	1.00
161_R	165_F	2.824	1.00
197_A	204_A	2.681	1.00
12_A	178_V	2.598	1.00
119_H	123_K	2.501	1.00
123_K	149_Y	2.445	1.00
130_P	151_E	2.392	1.00
10_I	203_Q	2.382	1.00
187_G	193_D	2.341	1.00
173_A	183_I	2.239	1.00
171_L	174_E	2.237	1.00
161_R	167_D	2.221	1.00
132_V	152_F	2.212	1.00
134_I	168_M	2.157	1.00
38_F	100_A	2.126	1.00
139_A	158_P	2.101	1.00
198_I	225_H	2.085	1.00
152_F	175_K	2.065	1.00
229_S	233_S	1.992	1.00
194_V	204_A	1.957	1.00
13_L	129_W	1.943	1.00
34_E	104_N	1.929	1.00
15_F	131_L	1.919	1.00
195_G	199_R	1.913	1.00
203_Q	225_H	1.868	1.00
126_A	151_E	1.824	1.00
184_L	205_C	1.790	1.00
173_A	202_M	1.784	1.00
14_T	185_H	1.755	1.00
179_P	182_E	1.750	1.00
185_H	197_A	1.711	1.00
124_Q	128_K	1.697	1.00
14_T	134_I	1.696	1.00
126_A	149_Y	1.694	1.00
10_I	184_L	1.651	1.00
12_A	176_L	1.649	1.00
118_T	231_L	1.618	1.00
178_V	183_I	1.605	1.00
14_T	172_A	1.583	1.00
173_A	180_I	1.580	1.00
131_L	150_F	1.536	1.00
13_L	186_V	1.516	1.00
208_R	229_S	1.503	1.00
132_V	176_L	1.466	1.00
115_P	209_P	1.445	1.00
39_V	100_A	1.434	1.00
13_L	125_L	1.421	1.00
205_C	228_I	1.414	1.00
20_T	186_V	1.364	1.00
17_L	22_Y	1.363	1.00
205_C	226_L	1.335	1.00
74_R	78_R	1.330	1.00
78_R	81_E	1.296	1.00
21_L	118_T	1.294	1.00
208_R	227_E	1.293	1.00
104_N	107_K	1.277	1.00
121_T	231_L	1.277	1.00
17_L	133_A	1.275	1.00
230_R	233_S	1.269	1.00
96_A	100_A	1.268	1.00
124_Q	127_K	1.264	1.00
100_A	104_N	1.251	1.00
38_F	104_N	1.249	1.00
166_S	170_F	1.235	1.00
154_L	175_K	1.231	1.00
117_Q	120_D	1.230	1.00
154_L	172_A	1.230	1.00
34_E	38_F	1.224	1.00
169_Y	196_G	1.223	1.00
169_Y	185_H	1.201	1.00
98_A	102_M	1.192	1.00
183_I	202_M	1.180	1.00
30_R	108_W	1.169	1.00
53_D	56_R	1.157	1.00
14_T	183_I	1.156	1.00
100_A	103_I	1.130	1.00
169_Y	202_M	1.122	1.00
35_A	39_V	1.121	1.00
134_I	172_A	1.119	1.00
167_D	171_L	1.115	1.00
37_T	43_H	1.114	1.00
114_V	146_L	1.111	1.00
126_A	131_L	1.107	1.00
12_A	183_I	1.097	1.00
99_H	103_I	1.095	1.00
12_A	130_P	1.093	1.00
120_D	232_A	1.089	1.00
139_A	155_R	1.076	1.00
78_R	82_Q	1.075	1.00
104_N	108_W	1.048	1.00
145_G	148_D	1.045	1.00
34_E	37_T	1.044	1.00
170_F	200_S	1.043	1.00
17_L	137_G	1.039	1.00
194_V	224_P	1.038	1.00
75_W	79_S	1.025	1.00
123_K	127_K	1.019	1.00
198_I	204_A	1.019	1.00
18_D	24_N	1.006	1.00
30_R	34_E	1.002	1.00
170_F	174_E	0.990	1.00
119_H	149_Y	0.989	1.00
167_D	170_F	0.988	1.00
18_D	137_G	0.986	1.00
135_T	155_R	0.984	1.00
34_E	108_W	0.972	1.00
185_H	202_M	0.962	1.00
170_F	180_I	0.960	1.00
172_A	176_L	0.959	1.00
122_L	150_F	0.954	1.00
114_V	119_H	0.946	1.00
33_R	37_T	0.937	1.00
154_L	171_L	0.936	1.00
101_A	105_F	0.930	1.00
203_Q	226_L	0.929	1.00
103_I	107_K	0.928	1.00
117_Q	230_R	0.926	1.00
71_D	74_R	0.921	1.00
169_Y	187_G	0.916	1.00
30_R	33_R	0.905	1.00
12_A	132_V	0.903	1.00
139_A	157_G	0.901	1.00
71_D	75_W	0.900	1.00
93_E	96_A	0.898	1.00
95_S	99_H	0.898	1.00
14_T	176_L	0.888	1.00
133_A	150_F	0.886	1.00
30_R	111_R	0.885	1.00
54_L	57_L	0.883	1.00
125_L	129_W	0.882	1.00
155_R	158_P	0.880	1.00
36_L	41_N	0.875	1.00
180_I	202_M	0.868	1.00
192_T	195_G	0.867	1.00
120_D	123_K	0.863	1.00
115_P	207_I	0.860	1.00
152_F	176_L	0.858	1.00
123_K	148_D	0.857	1.00
98_A	101_A	0.852	1.00
160_G	167_D	0.850	1.00
97_G	101_A	0.850	1.00
178_V	182_E	0.842	1.00
198_I	223_L	0.841	1.00
75_W	78_R	0.841	1.00
18_D	135_T	0.840	1.00
29_L	33_R	0.839	1.00
186_V	205_C	0.833	1.00
184_L	203_Q	0.828	1.00
228_I	234_L	0.824	1.00
14_T	202_M	0.821	1.00
205_C	234_L	0.804	1.00
81_E	85_L	0.804	1.00
189_D	192_T	0.804	1.00
125_L	131_L	0.803	1.00
10_I	129_W	0.800	1.00
77_F	81_E	0.799	1.00
76_R	79_S	0.798	1.00
72_V	75_W	0.797	1.00
204_A	225_H	0.793	1.00
11_S	129_W	0.789	1.00
159_H	171_L	0.788	1.00
194_V	206_W	0.788	1.00
82_Q	85_L	0.784	1.00
99_H	102_M	0.784	1.00
132_V	172_A	0.776	1.00
117_Q	232_A	0.772	1.00
219_D	223_L	0.767	1.00
168_M	172_A	0.761	1.00
119_H	145_G	0.759	1.00
90_S	93_E	0.754	1.00
75_W	80_I	0.753	1.00
206_W	227_E	0.751	1.00
75_W	83_A	0.746	1.00
84_M	87_A	0.745	1.00
115_P	118_T	0.743	1.00
219_D	222_L	0.738	1.00
136_N	162_S	0.734	1.00
122_L	149_Y	0.734	1.00
209_P	231_L	0.732	1.00
53_D	86_D	0.732	1.00
120_D	124_Q	0.729	1.00
196_G	200_S	0.724	1.00
10_I	182_E	0.720	1.00
130_P	178_V	0.720	1.00
11_S	178_V	0.718	1.00
14_T	132_V	0.712	1.00
169_Y	193_D	0.710	1.00
158_P	175_K	0.709	1.00
28_I	32_E	0.708	1.00
131_L	149_Y	0.708	1.00
19_D	25_R	0.702	1.00
131_L	151_E	0.698	1.00
74_R	77_F	0.696	1.00
33_R	44_P	0.694	1.00
22_Y	144_F	0.692	1.00
195_G	198_I	0.688	1.00
26_P	113_D	0.687	1.00
13_L	184_L	0.685	1.00
73_T	77_F	0.676	1.00
31_T	35_A	0.675	1.00
11_S	130_P	0.671	1.00
218_W	221_R	0.670	1.00
97_G	100_A	0.661	1.00
27_V	112_I	0.659	1.00
136_N	192_T	0.656	1.00
154_L	168_M	0.655	1.00
23_D	26_P	0.653	1.00
80_I	83_A	0.653	1.00
33_R	45_A	0.652	1.00
168_M	196_G	0.647	1.00
121_T	186_V	0.646	1.00
72_V	83_A	0.645	1.00
119_H	148_D	0.642	1.00
22_Y	112_I	0.640	1.00
152_F	172_A	0.638	1.00
185_H	193_D	0.637	1.00
74_R	79_S	0.629	1.00
102_M	106_A	0.628	1.00
150_F	153_V	0.626	1.00
23_D	113_D	0.626	1.00
134_I	185_H	0.623	1.00
118_T	122_L	0.623	1.00
117_Q	121_T	0.623	1.00
73_T	79_S	0.621	1.00
53_D	57_L	0.617	1.00
159_H	168_M	0.617	1.00
186_V	234_L	0.614	1.00
18_D	188_D	0.613	1.00
173_A	178_V	0.609	1.00
96_A	99_H	0.606	1.00
141_P	147_G	0.605	1.00
37_T	42_Y	0.604	1.00
39_V	96_A	0.602	1.00
71_D	79_S	0.601	1.00
228_I	231_L	0.599	1.00
92_E	96_A	0.599	1.00
185_H	196_G	0.597	1.00
20_T	207_I	0.597	1.00
118_T	121_T	0.594	1.00
108_W	111_R	0.593	1.00
180_I	183_I	0.593	1.00
166_S	199_R	0.592	1.00
173_A	200_S	0.591	1.00
152_F	155_R	0.590	1.00
72_V	76_R	0.589	1.00
76_R	80_I	0.588	1.00
82_Q	86_D	0.588	1.00
73_T	83_A	0.586	1.00
43_H	46_L	0.583	1.00
73_T	76_R	0.582	1.00
173_A	179_P	0.580	1.00
192_T	196_G	0.579	1.00
121_T	125_L	0.574	1.00
106_A	140_Q	0.572	1.00
26_P	30_R	0.571	1.00
23_D	115_P	0.569	1.00
28_I	137_G	0.569	1.00
74_R	82_Q	0.566	1.00
35_A	100_A	0.564	1.00
80_I	84_M	0.563	1.00
121_T	124_Q	0.562	1.00
123_K	126_A	0.560	1.00
24_N	137_G	0.556	1.00
31_T	104_N	0.555	1.00
114_V	144_F	0.552	1.00
117_Q	209_P	0.551	1.00
33_R	43_H	0.551	1.00
170_F	173_A	0.550	1.00
17_L	135_T	0.548	1.00
116_Q	232_A	0.547	1.00
126_A	148_D	0.547	1.00
14_T	169_Y	0.546	1.00
101_A	104_N	0.545	1.00
142_E	148_D	0.543	1.00
206_W	219_D	0.541	1.00
28_I	101_A	0.540	1.00
15_F	121_T	0.538	1.00
85_L	88_G	0.535	1.00
169_Y	197_A	0.534	1.00
39_V	97_G	0.533	1.00
21_L	133_A	0.531	1.00
20_T	193_D	0.529	1.00
103_I	106_A	0.528	1.00
13_L	131_L	0.527	1.00
134_I	154_L	0.527	1.00
136_N	164_P	0.526	1.00
121_T	228_I	0.523	1.00
73_T	78_R	0.523	1.00
156_A	168_M	0.518	1.00
10_I	13_L	0.517	1.00
207_I	231_L	0.516	1.00
116_Q	230_R	0.516	1.00
195_G	223_L	0.514	1.00
35_A	97_G	0.514	1.00
122_L	131_L	0.507	1.00
141_P	144_F	0.505	1.00
206_W	224_P	0.500	1.00
89_L	92_E	0.500	1.00

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
3vayA	2	0.9496	100	0.313	Contact Map
3ed5A	1	0.9286	100	0.33	Contact Map
4uw9A	1	0.8193	100	0.339	Contact Map
2om6A	2	0.9244	100	0.343	Contact Map
3umbA	2	0.9202	100	0.348	Contact Map
3smvA	1	0.9286	100	0.349	Contact Map
3qnmA	1	0.9286	100	0.351	Contact Map
3l5kA	1	0.8908	100	0.354	Contact Map
3s6jA	2	0.8697	100	0.356	Contact Map
1te2A	2	0.8739	100	0.356	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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