YBJG - ECOLI - GREMLIN Contacts

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YBJG - Putative undecaprenyl-diphosphatase YbjG

UniProt:	P75806	Sequences: MLENLNLSLFSLINATPDSAPWMISLAIFIAKDLITVVPLLAVVLWLWGLTAQRQLVIKIAIALAVSLFVSWTMGHLFPHDRPFVENIGYNFLHHAADDSFPSDHGTVIFTFALAFLCWHRLWSGSLLMVLAVVIAWSRVYLGVHWPLDMLGGLLAGMIGCLSAQIIWQAMGHKLYQRLQSWYRVCFALPIRKGWVRD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13676
Length:	198 (166)
Sequences:	7237 (5577)
Seq/√Len:	432.8

ECOLI - YBJG PGPB
BACSU - BCRC YODM
HALSA - Q9HRC2 Q9HNI3
SULSO - Q97VH2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_A	154_L	3.685	1.00
114_L	161_C	3.514	1.00
79_P	99_D	3.340	1.00
71_S	107_T	2.908	1.00
101_F	152_G	2.760	1.00
80_H	148_L	2.642	1.00
6_N	80_H	2.588	1.00
118_C	165_Q	2.476	1.00
67_S	111_T	2.451	1.00
66_V	160_G	2.352	1.00
74_M	78_F	2.346	1.00
110_F	132_A	2.327	1.00
67_S	107_T	2.267	1.00
24_I	141_Y	2.248	1.00
106_G	136_A	2.225	1.00
110_F	154_L	2.047	1.00
31_A	138_S	2.047	1.00
10_F	147_P	1.985	1.00
153_G	157_G	1.980	1.00
106_G	110_F	1.967	1.00
10_F	140_V	1.913	1.00
27_A	137_W	1.911	1.00
114_L	158_M	1.910	1.00
110_F	136_A	1.891	1.00
7_L	11_S	1.826	1.00
32_K	35_I	1.795	1.00
162_L	166_I	1.785	1.00
113_A	132_A	1.723	1.00
136_A	150_M	1.694	1.00
109_I	135_I	1.681	1.00
117_L	125_G	1.653	1.00
157_G	161_C	1.604	1.00
33_D	131_L	1.568	1.00
12_L	16_T	1.560	1.00
140_V	150_M	1.502	1.00
106_G	154_L	1.502	1.00
63_A	111_T	1.494	1.00
30_I	135_I	1.492	1.00
14_N	17_P	1.478	1.00
30_I	134_V	1.467	1.00
106_G	153_G	1.415	1.00
25_S	28_I	1.379	1.00
159_I	162_L	1.286	1.00
37_V	40_L	1.278	1.00
6_N	148_L	1.270	1.00
102_P	156_A	1.258	1.00
50_L	53_Q	1.230	1.00
68_L	72_W	1.228	1.00
45_L	49_G	1.223	1.00
125_G	128_L	1.210	1.00
107_T	156_A	1.197	1.00
158_M	162_L	1.195	1.00
126_S	130_V	1.190	1.00
27_A	138_S	1.189	1.00
113_A	128_L	1.188	1.00
78_F	101_F	1.186	1.00
75_G	104_D	1.179	1.00
80_H	146_W	1.172	1.00
74_M	102_P	1.165	1.00
38_V	41_L	1.163	1.00
160_G	164_A	1.151	1.00
53_Q	56_L	1.151	1.00
117_L	128_L	1.149	1.00
73_T	77_L	1.146	1.00
10_F	14_N	1.144	1.00
140_V	147_P	1.115	1.00
113_A	131_L	1.114	1.00
71_S	104_D	1.100	1.00
72_W	76_H	1.095	1.00
23_M	27_A	1.075	1.00
18_D	21_P	1.059	1.00
37_V	41_L	1.055	1.00
106_G	150_M	1.046	1.00
8_S	12_L	1.041	1.00
44_V	48_W	1.038	1.00
100_S	146_W	1.035	1.00
132_A	154_L	1.027	1.00
114_L	157_G	1.027	1.00
63_A	67_S	1.017	1.00
59_K	164_A	1.010	1.00
102_P	152_G	0.988	1.00
121_R	125_G	0.964	1.00
45_L	48_W	0.961	1.00
96_A	144_V	0.952	1.00
129_M	132_A	0.951	1.00
12_L	15_A	0.949	1.00
110_F	129_M	0.946	1.00
156_A	160_G	0.942	1.00
46_W	50_L	0.932	1.00
51_T	54_R	0.931	1.00
22_W	26_L	0.927	1.00
25_S	29_F	0.921	1.00
59_K	115_A	0.918	1.00
9_L	12_L	0.908	1.00
31_A	142_L	0.906	1.00
117_L	129_M	0.904	1.00
84_F	96_A	0.904	1.00
27_A	31_A	0.892	1.00
71_S	156_A	0.892	1.00
60_I	115_A	0.889	1.00
26_L	134_V	0.880	1.00
27_A	141_Y	0.873	1.00
109_I	132_A	0.870	1.00
31_A	35_I	0.868	1.00
131_L	135_I	0.859	1.00
165_Q	169_Q	0.858	1.00
115_A	119_W	0.857	1.00
69_F	73_T	0.853	1.00
154_L	158_M	0.849	1.00
29_F	32_K	0.842	1.00
18_D	22_W	0.839	1.00
110_F	161_C	0.834	1.00
51_T	55_Q	0.829	1.00
115_A	161_C	0.828	1.00
81_D	86_E	0.824	1.00
147_P	151_L	0.821	1.00
113_A	117_L	0.818	1.00
138_S	142_L	0.816	1.00
66_V	164_A	0.810	1.00
74_M	156_A	0.809	1.00
62_I	65_A	0.807	1.00
40_L	47_L	0.807	1.00
110_F	133_V	0.804	1.00
36_T	40_L	0.800	1.00
76_H	99_D	0.797	1.00
28_I	32_K	0.795	1.00
8_S	11_S	0.794	1.00
75_G	82_R	0.792	1.00
118_C	161_C	0.791	1.00
60_I	64_L	0.780	1.00
124_S	128_L	0.777	1.00
52_A	55_Q	0.773	1.00
77_L	81_D	0.769	1.00
34_L	135_I	0.768	1.00
55_Q	59_K	0.767	1.00
114_L	129_M	0.758	1.00
120_H	124_S	0.756	1.00
59_K	119_W	0.755	1.00
24_I	28_I	0.753	1.00
70_V	73_T	0.743	1.00
7_L	86_E	0.742	1.00
100_S	149_D	0.742	1.00
107_T	160_G	0.739	1.00
61_A	65_A	0.738	1.00
81_D	85_V	0.737	1.00
114_L	118_C	0.733	1.00
9_L	147_P	0.733	1.00
35_I	104_D	0.728	1.00
64_L	68_L	0.726	1.00
5_L	8_S	0.725	1.00
63_A	66_V	0.723	1.00
63_A	115_A	0.722	1.00
80_H	100_S	0.718	1.00
23_M	141_Y	0.714	1.00
64_L	108_V	0.713	1.00
137_W	141_Y	0.710	1.00
116_F	128_L	0.710	1.00
38_V	42_A	0.708	1.00
24_I	27_A	0.705	1.00
70_V	156_A	0.704	1.00
84_F	146_W	0.704	1.00
56_L	59_K	0.703	1.00
26_L	29_F	0.694	1.00
59_K	118_C	0.692	1.00
63_A	164_A	0.691	1.00
13_I	16_T	0.689	1.00
107_T	153_G	0.688	1.00
143_G	147_P	0.685	1.00
41_L	44_V	0.685	1.00
59_K	63_A	0.682	1.00
118_C	162_L	0.681	1.00
109_I	131_L	0.680	1.00
144_V	147_P	0.678	1.00
13_I	140_V	0.674	1.00
155_L	158_M	0.671	1.00
164_A	168_W	0.670	1.00
105_H	145_H	0.670	1.00
92_F	95_H	0.667	1.00
70_V	160_G	0.663	1.00
109_I	113_A	0.661	1.00
87_N	95_H	0.655	0.99
39_P	42_A	0.652	0.99
106_G	109_I	0.650	0.99
18_D	24_I	0.649	0.99
110_F	158_M	0.649	0.99
115_A	118_C	0.643	0.99
64_L	112_F	0.638	0.99
31_A	135_I	0.637	0.99
39_P	112_F	0.637	0.99
93_L	144_V	0.633	0.99
31_A	144_V	0.633	0.99
107_T	111_T	0.632	0.99
123_W	127_L	0.629	0.99
31_A	34_L	0.625	0.99
36_T	108_V	0.622	0.99
56_L	60_I	0.621	0.99
39_P	46_W	0.619	0.99
16_T	21_P	0.617	0.99
11_S	15_A	0.614	0.99
104_D	108_V	0.611	0.99
26_L	30_I	0.609	0.99
135_I	138_S	0.609	0.99
37_V	48_W	0.608	0.99
133_V	154_L	0.608	0.99
27_A	30_I	0.607	0.99
67_S	108_V	0.606	0.99
127_L	130_V	0.604	0.99
17_P	24_I	0.602	0.99
101_F	149_D	0.601	0.99
10_F	148_L	0.596	0.99
111_T	115_A	0.595	0.99
6_N	10_F	0.594	0.99
84_F	95_H	0.591	0.99
151_L	154_L	0.590	0.99
40_L	44_V	0.589	0.99
22_W	25_S	0.582	0.99
18_D	23_M	0.581	0.99
155_L	159_I	0.576	0.99
14_N	24_I	0.573	0.99
16_T	137_W	0.570	0.99
9_L	13_I	0.568	0.99
164_A	167_I	0.567	0.99
49_G	52_A	0.567	0.99
10_F	142_L	0.564	0.98
136_A	140_V	0.563	0.98
63_A	161_C	0.556	0.98
84_F	144_V	0.554	0.98
31_A	139_R	0.549	0.98
68_L	71_S	0.546	0.98
37_V	43_V	0.545	0.98
43_V	47_L	0.542	0.98
54_R	58_I	0.541	0.98
30_I	138_S	0.538	0.98
5_L	9_L	0.533	0.98
152_G	155_L	0.533	0.98
64_L	67_S	0.532	0.98
13_I	17_P	0.531	0.98
104_D	109_I	0.528	0.98
169_Q	172_G	0.527	0.98
33_D	36_T	0.525	0.98
111_T	161_C	0.524	0.98
21_P	25_S	0.524	0.98
14_N	146_W	0.519	0.97
41_L	45_L	0.518	0.97
14_N	143_G	0.518	0.97
85_V	146_W	0.513	0.97
58_I	62_I	0.507	0.97
120_H	128_L	0.506	0.97
10_F	13_I	0.500	0.97

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
4px7A	1	0.9697	100	0.362	Contact Map
1d2tA	5	0.9242	99.9	0.448	Contact Map
4citA	1	0.8889	99.9	0.458	Contact Map
2ipbA	2	0.9343	99.9	0.484	Contact Map
1qi9A	2	0.9596	99.9	0.491	Contact Map
1up8A	9	0.9394	99.9	0.506	Contact Map
3w36A	2	0.8586	99.9	0.511	Contact Map
3bb0A	1	0.9192	99.8	0.559	Contact Map
2kluA	1	0.2424	26.5	0.931	Contact Map
4mndA	2	0.6616	24.8	0.931	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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