YXBB - BACSU - GREMLIN Contacts

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YXBB - Uncharacterized protein YxbB

UniProt:	P46326	Sequences: MITAEECRTYKEFVDLYQSYLYPLLGARLSRMYSPKNKVIIDMGTGPGYLSIQLAKRTNAHVHAVDINPAMHEIAQEEAKKSGVSSLISFDLEDVHHLSYADQYADFIVSYSCLHHWEDVVKGLKECYRVLAPGGKIVILDTFNPQGSHLEIMRKQIKEPEYFRFVREAFEESYSFEDIHQFVQDAGIPNYSLETFHFLPEDFIESLDELEDAPLWEQNDQSTDHEIESVTWMLTIEKEKEGAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	244 (201)
Sequences:	14919 (10518)
Seq/√Len:	741.9

ECOLI - UBIE SMTA YJHP BIOC UBIG TAM CMOA TEHB YAFE CMOB RLMA
BACSU - YXBB MENG YCGJ YRRT YODH YBAJ YRHH YDAC YQEM YXJB
HALSA - Q9HR81 Q9HND6 Q9HMT2 Q9HR63 Q9HRX3 ARSM Q9HQ85 Q9HSK6
SULSO - Q7LXN7 Q97X57 Q97WT7 Q97ZU8 Q97WH3 Q97XD7 Q97WN4 Q97YX4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_V	61_H	3.174	1.00
128_Y	188_I	2.780	1.00
126_E	129_R	2.719	1.00
69_P	92_L	2.696	1.00
45_T	64_A	2.683	1.00
51_S	62_V	2.570	1.00
63_H	105_A	2.568	1.00
127_C	137_I	2.539	1.00
56_K	82_S	2.475	1.00
100_Y	105_A	2.410	1.00
106_D	132_A	2.365	1.00
121_V	185_D	2.339	1.00
44_G	113_C	2.331	1.00
75_A	90_F	2.330	1.00
65_V	93_E	2.327	1.00
38_K	107_F	2.326	1.00
72_H	90_F	2.275	1.00
61_H	89_S	2.091	1.00
74_I	77_E	2.069	1.00
72_H	76_Q	2.064	1.00
69_P	73_E	2.062	1.00
108_I	127_C	2.059	1.00
52_I	79_A	2.042	1.00
41_I	105_A	1.956	1.00
126_E	130_V	1.910	1.00
39_V	63_H	1.907	1.00
63_H	91_D	1.894	1.00
121_V	125_K	1.886	1.00
131_L	137_I	1.868	1.00
40_I	54_L	1.849	1.00
108_I	131_L	1.813	1.00
72_H	92_L	1.805	1.00
79_A	90_F	1.772	1.00
119_D	122_K	1.740	1.00
52_I	78_E	1.732	1.00
175_S	178_D	1.730	1.00
120_V	182_F	1.725	1.00
121_V	182_F	1.725	1.00
43_M	127_C	1.723	1.00
180_H	184_Q	1.676	1.00
45_T	51_S	1.670	1.00
66_D	72_H	1.614	1.00
27_A	53_Q	1.586	1.00
131_L	135_G	1.548	1.00
122_K	125_K	1.507	1.00
93_E	99_S	1.477	1.00
131_L	188_I	1.468	1.00
113_C	117_W	1.453	1.00
77_E	81_K	1.441	1.00
39_V	132_A	1.439	1.00
43_M	95_V	1.436	1.00
64_A	90_F	1.410	1.00
27_A	31_R	1.405	1.00
65_V	98_L	1.400	1.00
117_W	123_G	1.397	1.00
67_I	94_D	1.382	1.00
73_E	76_Q	1.379	1.00
99_S	126_E	1.352	1.00
202_D	206_S	1.344	1.00
63_H	89_S	1.340	1.00
41_I	108_I	1.334	1.00
70_A	73_E	1.328	1.00
80_K	85_S	1.325	1.00
110_S	113_C	1.305	1.00
102_D	129_R	1.302	1.00
51_S	64_A	1.277	1.00
29_L	138_V	1.274	1.00
39_V	105_A	1.264	1.00
181_Q	185_D	1.245	1.00
94_D	97_H	1.241	1.00
124_L	183_V	1.233	1.00
28_R	194_E	1.204	1.00
53_Q	57_R	1.199	1.00
101_A	104_Y	1.195	1.00
53_Q	56_K	1.195	1.00
44_G	110_S	1.195	1.00
108_I	130_V	1.194	1.00
40_I	107_F	1.193	1.00
91_D	100_Y	1.172	1.00
52_I	82_S	1.171	1.00
123_G	127_C	1.140	1.00
181_Q	184_Q	1.134	1.00
95_V	113_C	1.127	1.00
14_V	17_Y	1.108	1.00
48_G	75_A	1.105	1.00
28_R	32_M	1.098	1.00
45_T	75_A	1.096	1.00
74_I	78_E	1.094	1.00
65_V	91_D	1.094	1.00
112_S	116_H	1.092	1.00
77_E	80_K	1.086	1.00
98_L	130_V	1.081	1.00
55_A	87_L	1.070	1.00
66_D	71_M	1.065	1.00
121_V	186_A	1.060	1.00
39_V	104_Y	1.052	1.00
127_C	131_L	1.050	1.00
32_M	194_E	1.049	1.00
180_H	193_L	1.045	1.00
76_Q	80_K	1.041	1.00
64_A	75_A	1.023	1.00
78_E	82_S	1.019	1.00
42_D	64_A	1.018	1.00
27_A	57_R	1.016	1.00
38_K	60_A	1.010	1.00
14_V	18_Q	1.007	1.00
112_S	115_H	1.006	1.00
78_E	81_K	1.003	1.00
79_A	88_I	1.002	1.00
51_S	88_I	1.000	1.00
178_D	181_Q	0.992	1.00
176_F	195_T	0.979	1.00
128_Y	186_A	0.969	1.00
47_P	71_M	0.963	1.00
95_V	117_W	0.959	1.00
50_L	111_Y	0.946	1.00
98_L	126_E	0.945	1.00
114_L	141_D	0.944	1.00
52_I	56_K	0.944	1.00
125_K	186_A	0.941	1.00
115_H	141_D	0.936	1.00
40_I	62_V	0.922	1.00
73_E	77_E	0.920	1.00
35_P	38_K	0.919	1.00
48_G	90_F	0.917	1.00
41_I	130_V	0.912	1.00
125_K	129_R	0.910	1.00
37_N	60_A	0.901	1.00
31_R	57_R	0.897	1.00
107_F	135_G	0.875	1.00
38_K	106_D	0.870	1.00
45_T	66_D	0.864	1.00
28_R	31_R	0.864	1.00
97_H	122_K	0.856	1.00
158_K	162_Y	0.854	1.00
114_L	117_W	0.853	1.00
63_H	100_Y	0.852	1.00
51_S	90_F	0.848	1.00
56_K	84_V	0.847	1.00
32_M	192_S	0.846	1.00
54_L	109_V	0.844	1.00
11_K	68_N	0.843	1.00
68_N	71_M	0.829	1.00
160_P	164_R	0.820	1.00
152_I	155_K	0.813	1.00
50_L	109_V	0.803	1.00
182_F	186_A	0.803	1.00
104_Y	130_V	0.788	1.00
114_L	124_L	0.784	1.00
112_S	140_L	0.781	1.00
190_N	193_L	0.781	1.00
18_Q	47_P	0.780	1.00
10_Y	18_Q	0.779	1.00
9_T	12_E	0.779	1.00
55_A	88_I	0.777	1.00
122_K	126_E	0.775	1.00
42_D	116_H	0.774	1.00
40_I	109_V	0.772	1.00
124_L	179_I	0.770	1.00
76_Q	89_S	0.765	1.00
152_I	156_Q	0.764	1.00
43_M	108_I	0.763	1.00
111_Y	140_L	0.763	1.00
124_L	186_A	0.761	1.00
47_P	78_E	0.759	1.00
39_V	106_D	0.758	1.00
34_S	136_K	0.757	1.00
49_Y	53_Q	0.756	1.00
137_I	183_V	0.753	1.00
79_A	84_V	0.750	1.00
42_D	62_V	0.745	1.00
201_E	205_E	0.744	1.00
98_L	105_A	0.743	1.00
30_S	54_L	0.732	1.00
96_H	119_D	0.731	1.00
71_M	112_S	0.728	1.00
64_A	88_I	0.725	1.00
96_H	117_W	0.724	1.00
30_S	53_Q	0.719	1.00
110_S	117_W	0.713	1.00
18_Q	78_E	0.710	1.00
72_H	75_A	0.708	1.00
107_F	136_K	0.707	1.00
13_F	17_Y	0.704	1.00
20_Y	23_P	0.699	1.00
202_D	205_E	0.699	1.00
69_P	76_Q	0.695	1.00
29_L	111_Y	0.694	1.00
24_L	27_A	0.694	1.00
104_Y	132_A	0.689	1.00
102_D	126_E	0.688	1.00
114_L	123_G	0.687	1.00
52_I	55_A	0.686	1.00
33_Y	138_V	0.685	1.00
153_M	157_I	0.685	1.00
128_Y	187_G	0.683	1.00
79_A	83_G	0.674	1.00
55_A	84_V	0.673	1.00
105_A	130_V	0.672	1.00
203_F	206_S	0.670	1.00
61_H	87_L	0.669	1.00
116_H	141_D	0.668	1.00
50_L	54_L	0.663	1.00
12_E	16_L	0.661	1.00
10_Y	14_V	0.658	1.00
16_L	20_Y	0.654	1.00
144_N	175_S	0.648	1.00
43_M	65_V	0.645	1.00
139_I	183_V	0.644	1.00
26_G	50_L	0.642	1.00
30_S	57_R	0.641	1.00
103_Q	132_A	0.635	1.00
141_D	179_I	0.635	1.00
153_M	156_Q	0.628	1.00
17_Y	21_L	0.628	1.00
176_F	193_L	0.625	1.00
35_P	60_A	0.624	1.00
76_Q	90_F	0.622	1.00
183_V	186_A	0.619	1.00
102_D	130_V	0.618	1.00
16_L	19_S	0.617	1.00
19_S	22_Y	0.615	1.00
137_I	188_I	0.614	1.00
112_S	142_T	0.613	1.00
47_P	74_I	0.612	1.00
70_A	74_I	0.611	1.00
45_T	65_V	0.610	1.00
11_K	70_A	0.610	1.00
11_K	14_V	0.608	1.00
14_V	19_S	0.607	1.00
114_L	139_I	0.605	1.00
168_E	171_E	0.604	1.00
99_S	130_V	0.603	1.00
100_Y	104_Y	0.599	1.00
103_Q	133_P	0.599	1.00
114_L	179_I	0.599	1.00
104_Y	129_R	0.596	1.00
7_C	14_V	0.595	1.00
19_S	23_P	0.594	1.00
150_L	153_M	0.594	1.00
59_N	87_L	0.593	1.00
38_K	136_K	0.592	1.00
18_Q	22_Y	0.592	1.00
93_E	98_L	0.591	1.00
167_R	170_F	0.591	1.00
84_V	88_I	0.588	1.00
154_R	157_I	0.588	1.00
166_V	169_A	0.588	1.00
182_F	185_D	0.585	1.00
26_G	30_S	0.582	1.00
177_E	181_Q	0.576	1.00
30_S	33_Y	0.575	1.00
55_A	62_V	0.575	1.00
197_H	200_P	0.574	1.00
26_G	49_Y	0.572	1.00
42_D	45_T	0.568	1.00
176_F	180_H	0.565	1.00
49_Y	78_E	0.562	1.00
115_H	142_T	0.562	1.00
139_I	179_I	0.557	1.00
66_D	92_L	0.556	1.00
150_L	154_R	0.555	1.00
110_S	139_I	0.552	1.00
151_E	155_K	0.552	1.00
44_G	67_I	0.550	1.00
144_N	178_D	0.549	1.00
176_F	179_I	0.549	1.00
96_H	122_K	0.548	1.00
18_Q	21_L	0.546	1.00
200_P	203_F	0.545	1.00
165_F	168_E	0.543	1.00
51_S	55_A	0.539	1.00
97_H	126_E	0.539	1.00
152_I	157_I	0.538	1.00
129_R	132_A	0.535	1.00
136_K	139_I	0.534	1.00
35_P	107_F	0.524	1.00
111_Y	115_H	0.524	1.00
24_L	28_R	0.524	1.00
149_H	153_M	0.521	1.00
67_I	92_L	0.521	1.00
151_E	154_R	0.520	1.00
146_Q	177_E	0.516	1.00
30_S	58_T	0.514	1.00
196_F	203_F	0.513	1.00
95_V	123_G	0.512	1.00
35_P	58_T	0.512	1.00
45_T	90_F	0.511	1.00
52_I	88_I	0.510	1.00
42_D	109_V	0.509	1.00
71_M	111_Y	0.508	1.00
177_E	180_H	0.507	1.00
125_K	128_Y	0.506	1.00
37_N	107_F	0.504	1.00
164_R	167_R	0.504	1.00
100_Y	130_V	0.503	1.00
25_L	28_R	0.503	1.00
153_M	158_K	0.502	1.00
180_H	191_Y	0.502	1.00
164_R	168_E	0.501	1.00
178_D	182_F	0.500	1.00
33_Y	107_F	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
2o57A	2	0.959	100	0.407	Contact Map
4pneA	2	0.9467	100	0.412	Contact Map
4obxA	2	0.8402	100	0.42	Contact Map
3busA	1	0.8975	100	0.423	Contact Map
1vl5A	1	0.8648	100	0.432	Contact Map
3bkxA	2	0.9836	100	0.432	Contact Map
2fk8A	1	0.959	100	0.435	Contact Map
4ineA	2	0.959	100	0.437	Contact Map
3ujcA	1	0.9221	100	0.44	Contact Map
3hemA	2	0.9795	100	0.44	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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