UPPP - BACSU - GREMLIN Contacts

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UPPP - Undecaprenyl-diphosphatase

UniProt:	P94507	Sequences: MTLWELFVAAILGIVEGLTEYAPVSSTGHMIIVDDIWLKSSNLMSEEAANSFKVVIQLGSILAVAIVFKDRILNLLGLKKNITSDQEQGHKLSIAQIAVGLVPAAVLGFLFEDYIDEYLFSVKTVAIGLIAGAILMLFADWVNKRKTATDTLDRISYKQAIAVGLFQCLSLWPGFSRSGSTISGGVILGLNHRAAADFTFIMAMPIMMGASFLSLVKHWDSLSSDLMPFFIVGFICAFVVALFVVRFFLRLINKIKLVPFAIYRIILGVILLLIMM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	276 (257)
Sequences:	4127 (2695)
Seq/√Len:	168.1

ECOLI - UPPP
BACSU - UPPP
SULSO - UPPP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_R	197_D	3.557	1.00
100_G	198_F	3.376	1.00
166_F	184_G	3.004	1.00
5_E	8_V	2.832	1.00
15_V	33_V	2.824	1.00
105_A	209_G	2.695	1.00
72_I	204_M	2.670	1.00
10_A	236_C	2.547	1.00
141_W	258_V	2.518	1.00
130_I	268_G	2.406	1.00
101_L	206_I	2.355	1.00
191_N	194_A	2.340	1.00
16_E	60_S	2.308	1.00
133_A	265_I	2.278	1.00
134_I	138_F	2.272	1.00
250_R	254_K	2.253	1.00
116_D	214_S	2.240	1.00
185_G	190_L	2.233	1.00
212_F	216_V	2.181	1.00
104_A	206_I	2.104	1.00
14_I	240_V	2.034	1.00
112_E	214_S	1.989	1.00
161_I	165_L	1.975	1.00
213_L	217_K	1.968	1.00
69_K	73_L	1.876	1.00
126_A	268_G	1.848	1.00
99_V	157_Y	1.840	1.00
13_G	236_C	1.798	1.00
64_V	245_V	1.787	1.00
104_A	168_C	1.785	1.00
127_I	131_A	1.767	1.00
250_R	253_N	1.753	1.00
62_L	238_F	1.744	1.00
268_G	272_L	1.740	1.00
30_M	53_K	1.737	1.00
6_L	232_V	1.728	1.00
107_L	168_C	1.725	1.00
9_A	13_G	1.713	1.00
60_S	241_A	1.681	1.00
28_G	125_V	1.675	1.00
193_R	253_N	1.669	1.00
100_G	202_M	1.647	1.00
209_G	213_L	1.637	1.00
158_K	162_A	1.632	1.00
262_I	266_I	1.619	1.00
121_S	124_T	1.617	1.00
74_N	90_H	1.608	1.00
32_I	271_L	1.603	1.00
126_A	271_L	1.600	1.00
114_Y	118_Y	1.595	1.00
156_S	159_Q	1.582	1.00
67_V	246_R	1.564	1.00
128_G	172_W	1.542	1.00
12_L	33_V	1.535	1.00
58_L	211_S	1.530	1.00
236_C	240_V	1.523	1.00
138_F	142_V	1.522	1.00
126_A	272_L	1.518	1.00
12_L	30_M	1.489	1.00
75_L	94_I	1.488	1.00
92_L	96_Q	1.449	1.00
269_V	273_L	1.437	1.00
208_M	212_F	1.435	1.00
112_E	116_D	1.433	1.00
258_V	262_I	1.427	1.00
111_F	114_Y	1.424	1.00
137_L	258_V	1.423	1.00
270_I	274_I	1.413	1.00
4_W	8_V	1.403	1.00
111_F	115_I	1.386	1.00
105_A	109_F	1.350	1.00
123_K	127_I	1.318	1.00
213_L	216_V	1.316	1.00
135_L	183_S	1.310	1.00
9_A	52_F	1.308	1.00
159_Q	188_L	1.308	1.00
19_T	24_V	1.307	1.00
98_A	102_V	1.302	1.00
130_I	272_L	1.293	1.00
96_Q	157_Y	1.289	1.00
137_L	261_A	1.287	1.00
128_G	131_A	1.286	1.00
66_I	238_F	1.283	1.00
239_V	243_F	1.279	1.00
214_S	217_K	1.272	1.00
240_V	244_V	1.270	1.00
251_L	255_I	1.268	1.00
151_T	154_R	1.248	1.00
123_K	272_L	1.247	1.00
147_T	159_Q	1.241	1.00
51_S	218_H	1.234	1.00
46_E	50_N	1.221	1.00
107_L	111_F	1.218	1.00
112_E	217_K	1.217	1.00
51_S	55_V	1.203	1.00
49_A	53_K	1.201	1.00
68_F	249_L	1.201	1.00
124_T	128_G	1.193	1.00
9_A	232_V	1.186	1.00
9_A	229_F	1.177	1.00
44_M	49_A	1.173	1.00
231_I	235_I	1.171	1.00
181_T	199_T	1.171	1.00
238_F	242_L	1.168	1.00
11_I	15_V	1.166	1.00
105_A	108_G	1.164	1.00
91_K	95_A	1.160	1.00
101_L	105_A	1.156	1.00
175_F	180_S	1.156	1.00
57_Q	207_M	1.152	1.00
10_A	14_I	1.147	1.00
162_A	184_G	1.144	1.00
246_R	250_R	1.142	1.00
140_D	192_H	1.140	1.00
159_Q	190_L	1.134	1.00
6_L	228_P	1.132	1.00
251_L	259_P	1.126	1.00
70_D	73_L	1.121	1.00
157_Y	161_I	1.115	1.00
162_A	188_L	1.104	1.00
32_I	122_V	1.097	1.00
227_M	231_I	1.097	1.00
106_V	110_L	1.094	1.00
127_I	272_L	1.089	1.00
96_Q	160_A	1.088	1.00
29_H	263_Y	1.088	1.00
6_L	10_A	1.082	1.00
209_G	212_F	1.075	1.00
137_L	141_W	1.073	1.00
58_L	207_M	1.070	1.00
163_V	190_L	1.063	0.99
155_I	190_L	1.063	0.99
196_A	252_I	1.058	0.99
70_D	74_N	1.057	0.99
66_I	69_K	1.056	0.99
6_L	229_F	1.027	0.99
8_V	37_W	1.027	0.99
99_V	161_I	1.021	0.99
54_V	214_S	1.015	0.99
196_A	249_L	1.005	0.99
216_V	220_D	1.005	0.99
21_Y	241_A	1.001	0.99
248_F	255_I	0.995	0.99
67_V	249_L	0.995	0.99
259_P	262_I	0.992	0.99
185_G	195_A	0.992	0.99
14_I	18_L	0.990	0.99
33_V	37_W	0.988	0.99
226_L	229_F	0.986	0.99
93_S	201_I	0.985	0.99
65_A	72_I	0.984	0.99
114_Y	117_E	0.973	0.99
56_I	233_G	0.963	0.99
109_F	209_G	0.962	0.99
24_V	248_F	0.960	0.99
165_L	169_L	0.957	0.99
31_I	125_V	0.939	0.99
168_C	171_L	0.933	0.99
223_S	226_L	0.930	0.99
32_I	129_L	0.929	0.99
159_Q	185_G	0.924	0.99
54_V	210_A	0.923	0.99
244_V	247_F	0.921	0.99
232_V	236_C	0.914	0.98
59_G	234_F	0.912	0.98
132_G	169_L	0.911	0.98
249_L	252_I	0.910	0.98
104_A	171_L	0.901	0.98
159_Q	162_A	0.900	0.98
265_I	269_V	0.897	0.98
107_L	171_L	0.897	0.98
68_F	197_D	0.896	0.98
88_Q	91_K	0.895	0.98
163_V	202_M	0.889	0.98
132_G	264_R	0.884	0.98
224_S	228_P	0.884	0.98
115_I	171_L	0.874	0.98
67_V	242_L	0.872	0.98
228_P	231_I	0.870	0.98
139_A	187_I	0.863	0.98
122_V	271_L	0.862	0.98
242_L	246_R	0.862	0.98
266_I	270_I	0.861	0.98
135_L	139_A	0.855	0.98
124_T	172_W	0.853	0.98
78_L	95_A	0.853	0.98
137_L	265_I	0.853	0.98
104_A	108_G	0.851	0.98
9_A	236_C	0.851	0.98
45_S	49_A	0.847	0.97
196_A	248_F	0.841	0.97
32_I	267_L	0.838	0.97
88_Q	92_L	0.834	0.97
10_A	232_V	0.832	0.97
35_D	122_V	0.826	0.97
228_P	232_V	0.822	0.97
165_L	168_C	0.821	0.97
152_L	194_A	0.821	0.97
163_V	185_G	0.820	0.97
214_S	218_H	0.817	0.97
94_I	98_A	0.810	0.97
18_L	24_V	0.807	0.97
151_T	194_A	0.805	0.97
243_F	246_R	0.804	0.97
97_I	201_I	0.804	0.97
183_S	261_A	0.803	0.97
226_L	230_F	0.794	0.96
139_A	183_S	0.792	0.96
65_A	208_M	0.792	0.96
125_V	128_G	0.791	0.96
76_L	79_K	0.787	0.96
120_F	172_W	0.786	0.96
30_M	237_A	0.786	0.96
124_T	127_I	0.779	0.96
19_T	29_H	0.766	0.95
107_L	110_L	0.765	0.95
142_V	146_K	0.765	0.95
130_I	265_I	0.765	0.95
48_A	226_L	0.764	0.95
141_W	144_K	0.763	0.95
55_V	211_S	0.761	0.95
107_L	165_L	0.759	0.95
267_L	270_I	0.749	0.95
202_M	206_I	0.749	0.95
50_N	57_Q	0.745	0.95
136_M	179_G	0.744	0.95
264_R	271_L	0.744	0.95
162_A	165_L	0.735	0.94
136_M	140_D	0.735	0.94
155_I	194_A	0.735	0.94
50_N	116_D	0.734	0.94
55_V	234_F	0.727	0.94
142_V	145_R	0.725	0.94
140_D	257_L	0.725	0.94
95_A	98_A	0.725	0.94
61_I	204_M	0.724	0.94
27_T	57_Q	0.720	0.94
132_G	175_F	0.720	0.94
215_L	219_W	0.719	0.94
106_V	109_F	0.715	0.93
34_D	49_A	0.714	0.93
216_V	219_W	0.713	0.93
27_T	61_I	0.711	0.93
179_G	186_V	0.711	0.93
7_F	11_I	0.708	0.93
89_G	92_L	0.707	0.93
50_N	53_K	0.704	0.93
9_A	233_G	0.703	0.93
72_I	76_L	0.702	0.93
136_M	183_S	0.699	0.93
51_S	54_V	0.696	0.93
86_Q	91_K	0.690	0.92
93_S	152_L	0.690	0.92
27_T	30_M	0.689	0.92
96_Q	100_G	0.685	0.92
130_I	134_I	0.684	0.92
197_D	201_I	0.683	0.92
231_I	234_F	0.682	0.92
11_I	33_V	0.679	0.92
129_L	264_R	0.674	0.91
56_I	237_A	0.674	0.91
256_K	259_P	0.664	0.91
36_I	274_I	0.663	0.91
51_S	214_S	0.662	0.91
203_A	207_M	0.659	0.90
198_F	202_M	0.658	0.90
140_D	258_V	0.652	0.90
105_A	213_L	0.650	0.90
162_A	166_F	0.648	0.90
133_A	137_L	0.647	0.90
16_E	27_T	0.641	0.89
14_I	236_C	0.640	0.89
105_A	110_L	0.639	0.89
119_L	124_T	0.639	0.89
256_K	264_R	0.638	0.89
89_G	153_D	0.637	0.89
140_D	245_V	0.636	0.89
183_S	186_V	0.636	0.89
113_D	117_E	0.636	0.89
92_L	95_A	0.634	0.89
141_W	145_R	0.632	0.88
12_L	37_W	0.632	0.88
131_A	175_F	0.631	0.88
134_I	265_I	0.630	0.88
75_L	97_I	0.629	0.88
61_I	64_V	0.629	0.88
267_L	271_L	0.628	0.88
225_D	228_P	0.626	0.88
169_L	180_S	0.626	0.88
224_S	227_M	0.625	0.88
87_E	90_H	0.625	0.88
49_A	120_F	0.623	0.88
185_G	188_L	0.622	0.88
66_I	242_L	0.620	0.88
134_I	137_L	0.618	0.87
155_I	159_Q	0.617	0.87
11_I	37_W	0.617	0.87
57_Q	60_S	0.613	0.87
17_G	240_V	0.613	0.87
61_I	203_A	0.612	0.87
255_I	259_P	0.610	0.87
251_L	256_K	0.609	0.87
35_D	274_I	0.608	0.86
31_I	122_V	0.604	0.86
52_F	233_G	0.602	0.86
179_G	183_S	0.601	0.86
239_V	242_L	0.599	0.86
193_R	197_D	0.597	0.85
34_D	37_W	0.595	0.85
171_L	206_I	0.595	0.85
18_L	248_F	0.593	0.85
237_A	240_V	0.590	0.85
94_I	97_I	0.588	0.85
95_A	99_V	0.588	0.85
57_Q	61_I	0.586	0.84
151_T	191_N	0.585	0.84
86_Q	89_G	0.583	0.84
166_F	169_L	0.581	0.84
178_S	200_F	0.578	0.84
16_E	56_I	0.578	0.84
73_L	76_L	0.577	0.84
73_L	77_G	0.575	0.83
234_F	237_A	0.575	0.83
155_I	160_A	0.574	0.83
247_F	250_R	0.571	0.83
211_S	215_L	0.566	0.82
77_G	85_D	0.563	0.82
163_V	198_F	0.563	0.82
175_F	264_R	0.558	0.81
118_Y	124_T	0.558	0.81
264_R	267_L	0.557	0.81
62_L	234_F	0.557	0.81
172_W	175_F	0.554	0.81
70_D	77_G	0.554	0.81
131_A	135_L	0.554	0.81
16_E	61_I	0.551	0.81
77_G	88_Q	0.551	0.81
114_Y	119_L	0.549	0.80
21_Y	30_M	0.548	0.80
130_I	269_V	0.546	0.80
12_L	49_A	0.546	0.80
261_A	265_I	0.545	0.80
68_F	71_R	0.545	0.80
101_L	209_G	0.545	0.80
16_E	57_Q	0.544	0.80
100_G	155_I	0.542	0.80
132_G	172_W	0.540	0.79
125_V	129_L	0.540	0.79
258_V	261_A	0.539	0.79
91_K	94_I	0.538	0.79
24_V	129_L	0.538	0.79
261_A	264_R	0.536	0.79
136_M	257_L	0.535	0.79
137_L	262_I	0.534	0.79
110_L	114_Y	0.530	0.78
180_S	184_G	0.530	0.78
55_V	230_F	0.525	0.77
45_S	48_A	0.525	0.77
92_L	157_Y	0.524	0.77
183_S	202_M	0.524	0.77
192_H	256_K	0.523	0.77
215_L	218_H	0.522	0.77
64_V	204_M	0.522	0.77
104_A	115_I	0.521	0.77
103_P	108_G	0.520	0.77
136_M	256_K	0.520	0.77
152_L	203_A	0.519	0.77
170_S	234_F	0.519	0.77
34_D	53_K	0.519	0.77
115_I	172_W	0.517	0.76
137_L	140_D	0.516	0.76
182_I	257_L	0.516	0.76
192_H	252_I	0.515	0.76
110_L	113_D	0.515	0.76
56_I	207_M	0.513	0.76
140_D	186_V	0.509	0.75
28_G	32_I	0.506	0.75
152_L	155_I	0.505	0.75
95_A	157_Y	0.504	0.75
133_A	261_A	0.504	0.75
31_I	35_D	0.502	0.74
16_E	132_G	0.502	0.74
86_Q	147_T	0.500	0.74
168_C	172_W	0.500	0.74
109_F	213_L	0.500	0.74
65_A	204_M	0.500	0.74

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
4w252	1	0.2246	23.6	0.963	Contact Map
3mp7B	1	0.1957	16.7	0.965	Contact Map
2ww9B	1	0.2174	9.1	0.969	Contact Map
3ux4A	3	0.3768	6.9	0.971	Contact Map
3ne5A	3	0.808	5.7	0.972	Contact Map
3w9iA	3	0.7862	3.9	0.974	Contact Map
1jb0M	1	0.1123	3.9	0.974	Contact Map
4mt1A	3	0.8043	3.8	0.974	Contact Map
1rh5B	1	0.2029	3.7	0.974	Contact Map
1iflA	10	0.192	3.2	0.975	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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