YODM - BACSU - GREMLIN Contacts

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YODM - Putative lipid phosphate phosphatase YodM

UniProt:	O34349	Sequences: MYKPVSLFLFFLILAAAIHTNAVQSADEAISKAAVLIRQPWLNEVMTGITHLGASSFLLPLIVIIGAGMFFYRKTWDGLLMLLVFGTDRLLNKVLKEWIERVRPDFAPLVHESSFSFPSGHSMNAACVYPVIAYFLVKHLPFLSKHKKMVYIIAGVIAVLVGISRVYLGVHFVTDVLGGFSLGLLLFFLVKGFDEKIKRFRQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	203 (168)
Sequences:	6388 (4993)
Seq/√Len:	385.2

ECOLI - YBJG PGPB
BACSU - YODM BCRC
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
162_G	180_F	4.078	1.00
130_P	187_F	3.837	1.00
92_N	123_M	3.367	1.00
100_E	115_F	3.189	1.00
101_R	174_T	2.867	1.00
88_D	127_C	2.793	1.00
134_Y	191_K	2.722	1.00
87_T	186_L	2.615	1.00
95_L	99_I	2.596	1.00
117_F	178_G	2.556	1.00
43_N	167_Y	2.486	1.00
122_S	162_G	2.414	1.00
88_D	123_M	2.407	1.00
126_A	158_A	2.341	1.00
130_P	184_L	2.245	1.00
27_D	101_R	2.031	1.00
126_A	180_F	2.021	1.00
84_V	127_C	1.980	1.00
179_G	183_G	1.946	1.00
126_A	162_G	1.931	1.00
50_T	164_S	1.915	1.00
31_S	166_V	1.873	1.00
122_S	126_A	1.845	1.00
28_E	32_K	1.820	1.00
46_M	163_I	1.755	1.00
129_Y	158_A	1.737	1.00
122_S	180_F	1.737	1.00
35_V	38_R	1.733	1.00
122_S	179_G	1.711	1.00
125_A	161_V	1.698	1.00
188_F	192_G	1.669	1.00
166_V	176_V	1.663	1.00
162_G	176_V	1.661	1.00
31_S	173_V	1.612	1.00
133_A	151_Y	1.606	1.00
51_H	54_A	1.547	1.00
183_G	187_F	1.502	1.00
95_L	118_P	1.494	1.00
49_I	161_V	1.466	1.00
186_L	190_V	1.464	1.00
52_L	157_I	1.401	1.00
118_P	182_L	1.396	1.00
101_R	172_F	1.314	1.00
133_A	154_A	1.260	1.00
33_A	37_I	1.256	1.00
39_Q	42_L	1.256	1.00
155_G	158_A	1.244	1.00
96_K	120_G	1.224	1.00
137_V	151_Y	1.199	1.00
166_V	173_V	1.196	1.00
46_M	50_T	1.177	1.00
94_V	98_W	1.173	1.00
116_S	175_D	1.162	1.00
97_E	115_F	1.158	1.00
24_Q	28_E	1.155	1.00
49_I	160_L	1.148	1.00
123_M	182_L	1.131	1.00
38_R	43_N	1.121	1.00
134_Y	187_F	1.119	1.00
50_T	168_L	1.114	1.00
116_S	172_F	1.108	1.00
129_Y	154_A	1.104	1.00
92_N	120_G	1.095	1.00
93_K	97_E	1.080	1.00
67_A	71_F	1.065	1.00
129_Y	157_I	1.053	1.00
80_L	131_V	1.042	1.00
99_I	117_F	1.038	1.00
130_P	183_G	1.036	1.00
158_A	180_F	1.032	1.00
54_A	57_F	1.025	1.00
31_S	35_V	1.019	1.00
184_L	188_F	1.017	1.00
30_I	34_A	1.013	1.00
118_P	178_G	1.004	1.00
112_E	170_V	1.000	1.00
87_T	190_V	0.995	1.00
83_L	86_G	0.995	1.00
55_S	59_L	0.995	1.00
44_E	48_G	0.994	1.00
125_A	129_Y	0.993	1.00
126_A	187_F	0.992	1.00
44_E	47_T	0.988	1.00
42_L	46_M	0.977	1.00
70_F	73_R	0.974	1.00
37_I	40_P	0.963	1.00
96_K	103_R	0.957	1.00
117_F	175_D	0.947	1.00
29_A	33_A	0.945	1.00
151_Y	154_A	0.942	1.00
133_A	155_G	0.941	1.00
80_L	190_V	0.939	1.00
133_A	136_L	0.938	1.00
41_W	45_V	0.933	1.00
58_L	128_V	0.932	1.00
125_A	158_A	0.927	1.00
26_A	29_A	0.926	1.00
70_F	74_K	0.918	1.00
126_A	184_L	0.914	1.00
91_L	186_L	0.909	1.00
68_G	72_Y	0.907	1.00
185_L	188_F	0.905	1.00
148_K	152_I	0.902	1.00
180_F	184_L	0.902	1.00
89_R	93_K	0.897	1.00
81_M	131_V	0.894	1.00
73_R	76_W	0.887	1.00
98_W	102_V	0.887	1.00
57_F	60_P	0.885	1.00
160_L	164_S	0.871	1.00
101_R	116_S	0.863	1.00
46_M	164_S	0.862	1.00
22_A	25_S	0.855	1.00
25_S	29_A	0.850	1.00
34_A	166_V	0.848	1.00
43_N	47_T	0.848	1.00
130_P	155_G	0.844	1.00
84_V	87_T	0.840	1.00
33_A	36_L	0.840	1.00
84_V	187_F	0.833	1.00
81_M	85_F	0.828	1.00
131_V	134_Y	0.828	1.00
130_P	134_Y	0.821	1.00
57_F	61_L	0.820	1.00
74_K	77_D	0.818	1.00
121_H	171_H	0.817	1.00
126_A	159_V	0.815	1.00
30_I	33_A	0.807	1.00
68_G	71_F	0.802	1.00
182_L	186_L	0.799	1.00
191_K	195_E	0.784	1.00
56_S	59_L	0.774	1.00
34_A	37_I	0.773	1.00
30_I	166_V	0.767	1.00
129_Y	133_A	0.766	1.00
47_T	51_H	0.765	1.00
159_V	180_F	0.764	1.00
122_S	176_V	0.762	1.00
88_D	186_L	0.758	1.00
105_D	110_V	0.756	1.00
66_G	70_F	0.754	1.00
59_L	63_V	0.750	1.00
45_V	160_L	0.749	1.00
84_V	131_V	0.748	1.00
50_T	54_A	0.736	1.00
136_L	154_A	0.732	1.00
190_V	194_D	0.730	1.00
84_V	88_D	0.727	1.00
46_M	49_I	0.727	1.00
80_L	83_L	0.724	1.00
173_V	177_L	0.723	1.00
46_M	167_Y	0.721	1.00
45_V	48_G	0.718	1.00
152_I	156_V	0.718	1.00
126_A	155_G	0.713	1.00
28_E	34_A	0.711	1.00
53_G	161_V	0.705	1.00
131_V	135_F	0.698	1.00
150_V	154_A	0.696	0.99
29_A	32_K	0.695	0.99
88_D	92_N	0.694	0.99
192_G	196_K	0.694	0.99
34_A	169_G	0.693	0.99
95_L	182_L	0.691	0.99
111_H	114_S	0.690	0.99
80_L	134_Y	0.686	0.99
70_F	75_T	0.685	0.99
83_L	194_D	0.680	0.99
48_G	51_H	0.680	0.99
157_I	161_V	0.680	0.99
85_F	88_D	0.677	0.99
56_S	60_P	0.677	0.99
80_L	84_V	0.677	0.99
122_S	125_A	0.672	0.99
88_D	124_N	0.672	0.99
181_S	184_L	0.670	0.99
50_T	165_R	0.668	0.99
69_M	74_K	0.668	0.99
106_F	109_L	0.667	0.99
21_N	24_Q	0.661	0.99
91_L	182_L	0.661	0.99
120_G	171_H	0.659	0.99
163_I	167_Y	0.659	0.99
174_T	178_G	0.651	0.99
100_E	114_S	0.649	0.99
132_I	154_A	0.647	0.99
84_V	190_V	0.647	0.99
105_D	111_H	0.647	0.99
90_L	94_V	0.641	0.99
123_M	179_G	0.635	0.99
131_V	187_F	0.628	0.99
25_S	28_E	0.628	0.99
127_C	131_V	0.627	0.99
37_I	163_I	0.626	0.99
77_D	80_L	0.626	0.99
125_A	157_I	0.626	0.99
27_D	174_T	0.623	0.99
31_S	34_A	0.616	0.99
92_N	182_L	0.616	0.99
90_L	93_K	0.616	0.99
30_I	173_V	0.613	0.99
77_D	81_M	0.610	0.99
85_F	128_V	0.596	0.98
40_P	43_N	0.595	0.98
67_A	70_F	0.592	0.98
21_N	25_S	0.591	0.98
105_D	109_L	0.588	0.98
66_G	82_L	0.587	0.98
42_L	167_Y	0.585	0.98
84_V	91_L	0.583	0.98
101_R	175_D	0.579	0.98
102_V	114_S	0.578	0.98
162_G	166_V	0.573	0.98
80_L	194_D	0.568	0.98
55_S	60_P	0.567	0.98
69_M	73_R	0.558	0.98
89_R	92_N	0.556	0.98
193_F	196_K	0.551	0.97
43_N	46_M	0.551	0.97
23_V	26_A	0.551	0.97
149_M	153_I	0.547	0.97
39_Q	44_E	0.544	0.97
123_M	127_C	0.542	0.97
112_E	115_F	0.540	0.97
101_R	117_F	0.539	0.97
174_T	177_L	0.539	0.97
108_P	112_E	0.538	0.97
112_E	124_N	0.537	0.97
190_V	193_F	0.535	0.97
76_W	80_L	0.524	0.96
71_F	74_K	0.521	0.96
134_Y	195_E	0.520	0.96
137_V	147_K	0.520	0.96
122_S	170_V	0.519	0.96
131_V	191_K	0.517	0.96
63_V	82_L	0.515	0.96
69_M	72_Y	0.515	0.96
35_V	169_G	0.514	0.96
170_V	173_V	0.513	0.96
178_G	181_S	0.512	0.96
31_S	168_L	0.512	0.96
87_T	90_L	0.512	0.96
187_F	191_K	0.508	0.96
130_P	188_F	0.507	0.96
22_A	28_E	0.506	0.96
164_S	168_L	0.505	0.96
47_T	168_L	0.502	0.96
161_V	164_S	0.502	0.96
32_K	36_L	0.501	0.95
134_Y	188_F	0.501	0.95
123_M	158_A	0.501	0.95
70_F	78_G	0.500	0.95

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	0.9015	100	0.355	Contact Map
1qi9A	2	0.9163	99.9	0.455	Contact Map
1up8A	9	0.9261	99.9	0.457	Contact Map
1d2tA	5	0.9458	99.9	0.464	Contact Map
4citA	1	0.9557	99.9	0.478	Contact Map
2ipbA	2	0.9458	99.9	0.48	Contact Map
3w36A	2	0.9507	99.8	0.513	Contact Map
3bb0A	1	0.9557	99.7	0.555	Contact Map
2kluA	1	0.1724	25.1	0.925	Contact Map
2m20A	2	0.1527	8	0.94	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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