YHBO - ECOLI - GREMLIN Contacts

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YHBO - Protein YhbO

UniProt:	P45470	Sequences: MSKKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREALRLLGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12784
Length:	172 (161)
Sequences:	14461 (9772)
Seq/√Len:	770.1

ECOLI - YHBO YAJL HCHA
BACSU - YRAA GS18 YOAZ YDEA
HALSA - Q9HMG4 Q9HRT2
SULSO - Q97Z65

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
165_E	168_R	2.657	1.00
4_K	31_E	2.639	1.00
6_A	66_F	2.553	1.00
145_V	169_L	2.552	1.00
33_I	66_F	2.384	1.00
6_A	35_I	2.355	1.00
119_R	147_K	2.349	1.00
120_K	139_Y	2.319	1.00
116_I	121_L	2.235	1.00
4_K	33_I	2.072	1.00
42_T	53_T	2.042	1.00
119_R	146_D	2.040	1.00
33_I	56_K	2.009	1.00
145_V	165_E	1.909	1.00
24_E	167_L	1.892	1.00
120_K	141_Q	1.839	1.00
117_R	137_E	1.835	1.00
28_A	167_L	1.821	1.00
128_I	132_K	1.766	1.00
94_V	149_Q	1.755	1.00
22_A	26_R	1.751	1.00
120_K	137_E	1.716	1.00
119_R	150_L	1.628	1.00
94_V	100_V	1.582	1.00
145_V	151_V	1.581	1.00
93_F	98_K	1.572	1.00
44_K	51_S	1.552	1.00
130_D	134_A	1.523	1.00
99_P	169_L	1.501	1.00
102_A	152_T	1.498	1.00
37_K	83_D	1.479	1.00
101_F	166_A	1.477	1.00
15_D	19_T	1.471	1.00
68_A	99_P	1.469	1.00
57_S	60_E	1.440	1.00
153_S	158_D	1.416	1.00
59_D	85_R	1.409	1.00
88_T	92_D	1.405	1.00
7_V	70_L	1.403	1.00
151_V	169_L	1.397	1.00
120_K	146_D	1.392	1.00
89_F	93_F	1.390	1.00
7_V	22_A	1.380	1.00
87_V	91_R	1.378	1.00
130_D	133_N	1.375	1.00
102_A	110_L	1.371	1.00
42_T	51_S	1.356	1.00
36_E	39_A	1.352	1.00
45_G	48_G	1.306	1.00
131_V	136_A	1.303	1.00
92_D	96_S	1.295	1.00
88_T	91_R	1.293	1.00
84_N	88_T	1.288	1.00
121_L	138_F	1.287	1.00
145_V	149_Q	1.277	1.00
13_F	18_F	1.270	1.00
94_V	115_V	1.251	1.00
112_S	134_A	1.244	1.00
94_V	150_L	1.235	1.00
13_F	45_G	1.227	1.00
97_G	149_Q	1.226	1.00
85_R	88_T	1.224	1.00
165_E	169_L	1.218	1.00
131_V	140_D	1.215	1.00
51_S	55_D	1.215	1.00
101_F	162_F	1.212	1.00
119_R	149_Q	1.209	1.00
25_F	163_N	1.202	1.00
5_I	68_A	1.162	1.00
9_I	34_T	1.162	1.00
23_D	27_K	1.153	1.00
87_V	113_A	1.147	1.00
20_S	160_P	1.134	1.00
56_K	60_E	1.127	1.00
16_S	20_S	1.127	1.00
97_G	100_V	1.125	1.00
11_D	44_K	1.123	1.00
18_F	34_T	1.116	1.00
142_E	161_A	1.095	1.00
128_I	140_D	1.086	1.00
105_H	127_I	1.081	1.00
9_I	18_F	1.075	1.00
20_S	23_D	1.072	1.00
108_Q	130_D	1.071	1.00
82_G	112_S	1.070	1.00
70_L	162_F	1.066	1.00
92_D	95_N	1.065	1.00
91_R	95_N	1.057	1.00
120_K	144_V	1.056	1.00
22_A	34_T	1.052	1.00
67_D	98_K	1.050	1.00
114_D	117_R	1.045	1.00
8_L	86_F	1.043	1.00
151_V	162_F	1.041	1.00
94_V	97_G	1.031	1.00
45_G	49_E	1.025	1.00
39_A	57_S	1.022	1.00
111_I	138_F	1.011	1.00
20_S	163_N	0.998	1.00
93_F	96_S	0.995	1.00
143_V	165_E	0.979	1.00
153_S	162_F	0.976	1.00
99_P	149_Q	0.961	1.00
102_A	107_P	0.953	1.00
24_E	163_N	0.947	1.00
37_K	85_R	0.944	1.00
7_V	32_V	0.944	1.00
81_R	112_S	0.938	1.00
154_R	158_D	0.930	1.00
124_V	155_T	0.929	1.00
71_L	90_T	0.924	1.00
56_K	61_V	0.911	1.00
129_I	133_N	0.910	1.00
99_P	151_V	0.902	1.00
21_P	70_L	0.898	1.00
35_I	56_K	0.898	1.00
5_I	30_H	0.886	1.00
30_H	68_A	0.881	1.00
71_L	109_L	0.880	1.00
160_P	164_R	0.874	1.00
23_D	26_R	0.867	1.00
151_V	166_A	0.864	1.00
21_P	159_L	0.862	1.00
112_S	135_G	0.849	1.00
20_S	159_L	0.847	1.00
127_I	130_D	0.846	1.00
87_V	112_S	0.833	1.00
30_H	167_L	0.827	1.00
107_P	123_A	0.827	1.00
70_L	101_F	0.826	1.00
22_A	32_V	0.822	1.00
18_F	22_A	0.822	1.00
68_A	166_A	0.806	1.00
64_A	92_D	0.802	1.00
35_I	61_V	0.802	1.00
71_L	106_G	0.799	1.00
9_I	13_F	0.799	1.00
24_E	164_R	0.795	1.00
71_L	86_F	0.793	1.00
129_I	132_K	0.792	1.00
131_V	135_G	0.788	1.00
89_F	92_D	0.782	1.00
36_E	54_I	0.780	1.00
68_A	101_F	0.778	1.00
15_D	45_G	0.774	1.00
13_F	52_V	0.774	1.00
132_K	142_E	0.773	1.00
11_D	38_Q	0.772	1.00
25_F	166_A	0.770	1.00
15_D	49_E	0.770	1.00
91_R	113_A	0.768	1.00
69_L	93_F	0.766	1.00
13_F	72_P	0.764	1.00
83_D	86_F	0.764	1.00
99_P	166_A	0.751	1.00
151_V	165_E	0.750	1.00
103_I	159_L	0.736	1.00
66_F	93_F	0.727	1.00
7_V	18_F	0.725	1.00
87_V	90_T	0.715	1.00
37_K	58_I	0.707	1.00
122_T	144_V	0.699	1.00
117_R	135_G	0.693	1.00
42_T	54_I	0.691	1.00
15_D	47_K	0.685	1.00
161_A	164_R	0.678	1.00
118_G	137_E	0.672	1.00
90_T	109_L	0.668	1.00
24_E	28_A	0.661	1.00
79_Y	82_G	0.660	1.00
61_V	66_F	0.657	1.00
102_A	106_G	0.655	1.00
84_N	87_V	0.655	1.00
90_T	113_A	0.652	1.00
87_V	109_L	0.652	1.00
39_A	54_I	0.651	1.00
108_Q	127_I	0.641	1.00
24_E	27_K	0.637	1.00
110_L	113_A	0.634	1.00
25_F	30_H	0.633	1.00
123_A	138_F	0.631	1.00
121_L	136_A	0.630	1.00
103_I	162_F	0.621	1.00
9_I	43_V	0.619	1.00
124_V	127_I	0.615	1.00
94_V	119_R	0.609	1.00
17_E	73_G	0.609	1.00
6_A	61_V	0.608	1.00
65_E	96_S	0.605	1.00
26_R	32_V	0.605	1.00
116_I	122_T	0.601	1.00
5_I	25_F	0.601	1.00
135_G	138_F	0.601	1.00
161_A	165_E	0.600	1.00
17_E	156_P	0.593	1.00
111_I	131_V	0.592	1.00
100_V	149_Q	0.589	1.00
123_A	127_I	0.589	1.00
164_R	168_R	0.588	1.00
64_A	96_S	0.588	1.00
44_K	48_G	0.585	1.00
6_A	89_F	0.585	1.00
46_K	49_E	0.582	1.00
159_L	163_N	0.581	1.00
20_S	24_E	0.576	1.00
121_L	131_V	0.574	1.00
128_I	142_E	0.572	1.00
80_L	83_D	0.568	1.00
36_E	55_D	0.567	1.00
76_S	80_L	0.562	1.00
66_F	69_L	0.561	1.00
4_K	67_D	0.560	1.00
14_E	23_D	0.557	1.00
15_D	52_V	0.556	1.00
82_G	87_V	0.555	1.00
139_Y	144_V	0.544	1.00
143_V	151_V	0.542	1.00
141_Q	144_V	0.541	1.00
54_I	57_S	0.540	1.00
91_R	115_V	0.540	1.00
78_D	82_G	0.540	1.00
33_I	55_D	0.536	1.00
101_F	151_V	0.534	1.00
24_E	160_P	0.532	1.00
107_P	131_V	0.532	1.00
100_V	150_L	0.529	1.00
74_G	109_L	0.527	1.00
122_T	138_F	0.527	1.00
111_I	116_I	0.526	1.00
7_V	21_P	0.524	1.00
70_L	153_S	0.524	1.00
61_V	89_F	0.522	1.00
125_K	155_T	0.516	1.00
8_L	69_L	0.514	1.00
143_V	162_F	0.514	1.00
136_A	140_D	0.513	1.00
18_F	72_P	0.513	1.00
44_K	55_D	0.507	1.00
14_E	46_K	0.506	1.00
40_G	43_V	0.502	1.00
110_L	150_L	0.500	1.00
12_E	44_K	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
1oi4A	2	0.9884	100	0.14	Contact Map
3ewnA	2	0.9767	100	0.164	Contact Map
3noqA	2	0.9709	100	0.164	Contact Map
3fseA	2	0.9826	100	0.167	Contact Map
3l18A	2	0.9767	100	0.172	Contact Map
2rk3A	2	0.9826	100	0.173	Contact Map
2vrnA	2	0.9826	100	0.174	Contact Map
4e08A	2	0.9826	100	0.174	Contact Map
3mgkA	2	0.9651	100	0.175	Contact Map
4oggA	3	0.9767	100	0.18	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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