PPAX - BACSU - GREMLIN Contacts

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PPAX - Pyrophosphatase PpaX

UniProt:	Q9JMQ2	Sequences: MSDKQVTTILFDLDGTLINTNELIIASFLHTLEHYYPSKYKREDVLAFIGPSLFDTFSSMDPDKCEDMIAMYRAYNHDMHDSLVTEYETVYETLDALKKAGFTLGIVTTKLRDTVNMGLKLTGIGEFFETVVTLDDVTNAKPDPEPVLLALKQLGSEPAEAIMVGDNYHDVLAGKNAGTKTAGVAWTIKGPEMLAKHEPDFMLEKMSDLLQIVGVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	216 (201)
Sequences:	30439 (23734)
Seq/√Len:	1674.1

ECOLI - GPH YNIC YRFG YIEH YFBT YIGB YJJG PGMB YQAB YIHX
BACSU - PPAX YHCW YSAA PGMB YFNB
HALSA - Q9HSS2 Q9HQE2 Q9HP74 Q9HMC4
SULSO - Q7LXL6 Q97ZU6 Q7LX46 Q97WT6 Q97YZ1 Q97X58

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_T	160_E	4.215	1.00
149_L	153_Q	2.801	1.00
120_K	125_G	2.776	1.00
139_N	143_D	2.699	1.00
165_G	170_D	2.644	1.00
174_G	181_T	2.588	1.00
95_D	127_F	2.463	1.00
8_T	156_S	2.427	1.00
112_R	116_N	2.415	1.00
6_V	180_K	2.340	1.00
91_Y	95_D	2.303	1.00
105_G	130_T	2.273	1.00
149_L	152_K	2.235	1.00
103_T	129_E	2.231	1.00
112_R	136_D	2.128	1.00
108_T	115_V	2.125	1.00
151_L	161_A	2.110	1.00
175_K	200_D	2.100	1.00
11_F	104_L	2.074	1.00
107_V	146_P	2.058	1.00
204_E	208_D	2.021	1.00
34_H	71_M	2.005	1.00
139_N	145_E	1.948	1.00
130_T	153_Q	1.938	1.00
171_V	181_T	1.938	1.00
172_L	176_N	1.828	1.00
41_K	44_D	1.813	1.00
157_E	160_E	1.789	1.00
98_K	129_E	1.763	1.00
180_K	200_D	1.722	1.00
30_H	75_Y	1.715	1.00
9_I	102_F	1.714	1.00
151_L	179_T	1.711	1.00
98_K	127_F	1.652	1.00
10_L	163_M	1.651	1.00
162_I	182_A	1.635	1.00
104_L	128_F	1.629	1.00
163_M	174_G	1.603	1.00
96_A	100_A	1.600	1.00
10_L	150_A	1.550	1.00
90_V	206_M	1.549	1.00
151_L	158_P	1.515	1.00
156_S	161_A	1.508	1.00
185_A	204_E	1.507	1.00
8_T	154_L	1.482	1.00
10_L	107_V	1.475	1.00
116_N	125_G	1.465	1.00
105_G	154_L	1.414	1.00
6_V	162_I	1.405	1.00
9_I	97_L	1.403	1.00
168_Y	172_L	1.356	1.00
9_I	164_V	1.347	1.00
87_Y	186_W	1.344	1.00
93_T	206_M	1.343	1.00
182_A	203_L	1.335	1.00
34_H	75_Y	1.309	1.00
96_A	99_K	1.304	1.00
185_A	202_M	1.283	1.00
35_Y	71_M	1.283	1.00
144_P	148_L	1.265	1.00
205_K	208_D	1.254	1.00
75_Y	78_D	1.246	1.00
13_L	106_I	1.242	1.00
13_L	115_V	1.234	1.00
89_T	92_E	1.233	1.00
191_P	195_A	1.231	1.00
55_D	58_S	1.228	1.00
71_M	74_A	1.224	1.00
30_H	34_H	1.209	1.00
13_L	18_I	1.208	1.00
132_V	153_Q	1.204	1.00
116_N	120_K	1.199	1.00
30_H	79_M	1.199	1.00
17_L	90_V	1.190	1.00
16_T	164_V	1.189	1.00
182_A	201_F	1.182	1.00
115_V	133_T	1.160	1.00
71_M	75_Y	1.147	1.00
10_L	161_A	1.141	1.00
132_V	150_A	1.139	1.00
70_A	74_A	1.124	1.00
92_E	207_S	1.115	1.00
75_Y	79_M	1.113	1.00
147_V	163_M	1.107	1.00
8_T	161_A	1.106	1.00
67_D	71_M	1.095	1.00
161_A	179_T	1.084	1.00
8_T	103_T	1.082	1.00
42_R	46_L	1.073	1.00
95_D	99_K	1.071	1.00
148_L	152_K	1.061	1.00
147_V	173_A	1.051	1.00
31_T	35_Y	1.051	1.00
98_K	104_L	1.042	1.00
26_A	79_M	1.036	1.00
86_E	124_I	1.034	1.00
54_F	58_S	1.027	1.00
26_A	30_H	1.023	1.00
175_K	181_T	1.021	1.00
14_D	20_T	1.014	1.00
106_I	128_F	1.011	1.00
94_L	128_F	1.003	1.00
13_L	110_K	1.000	1.00
147_V	179_T	0.999	1.00
30_H	33_E	0.998	1.00
145_E	149_L	0.995	1.00
112_R	133_T	0.992	1.00
107_V	150_A	0.987	1.00
173_A	177_A	0.984	1.00
92_E	95_D	0.983	1.00
150_A	154_L	0.978	1.00
171_V	199_P	0.971	1.00
130_T	154_L	0.969	1.00
74_A	78_D	0.967	1.00
115_V	118_G	0.965	1.00
29_L	33_E	0.964	1.00
8_T	105_G	0.961	1.00
163_M	179_T	0.960	1.00
10_L	179_T	0.954	1.00
123_G	126_E	0.950	1.00
191_P	204_E	0.946	1.00
117_M	121_L	0.935	1.00
55_D	59_S	0.935	1.00
91_Y	127_F	0.935	1.00
108_T	133_T	0.925	1.00
147_V	165_G	0.919	1.00
148_L	177_A	0.912	1.00
145_E	148_L	0.908	1.00
117_M	120_K	0.904	1.00
14_D	108_T	0.902	1.00
89_T	205_K	0.898	1.00
169_H	172_L	0.897	1.00
180_K	201_F	0.896	1.00
14_D	110_K	0.892	1.00
95_D	126_E	0.882	1.00
10_L	154_L	0.876	1.00
137_V	149_L	0.870	1.00
183_G	194_L	0.869	1.00
32_L	37_P	0.869	1.00
112_R	135_D	0.868	1.00
26_A	83_L	0.866	1.00
40_Y	44_D	0.860	1.00
203_L	209_L	0.854	1.00
94_L	127_F	0.849	1.00
138_T	145_E	0.849	1.00
43_E	47_A	0.849	1.00
26_A	29_L	0.847	1.00
158_P	179_T	0.845	1.00
97_L	102_F	0.842	1.00
86_E	91_Y	0.841	1.00
57_F	61_D	0.834	1.00
148_L	158_P	0.831	1.00
104_L	127_F	0.831	1.00
105_G	150_A	0.831	1.00
66_E	70_A	0.829	1.00
164_V	182_A	0.828	1.00
6_V	102_F	0.826	1.00
9_I	162_I	0.819	1.00
162_I	180_K	0.816	1.00
132_V	149_L	0.815	1.00
51_P	59_S	0.812	1.00
13_L	118_G	0.810	1.00
175_K	198_E	0.806	1.00
87_Y	90_V	0.792	1.00
192_E	195_A	0.791	1.00
110_K	115_V	0.787	1.00
181_T	200_D	0.783	1.00
87_Y	184_V	0.783	1.00
58_S	65_C	0.782	1.00
97_L	104_L	0.779	1.00
14_D	166_D	0.773	1.00
79_M	82_S	0.770	1.00
7_T	102_F	0.767	1.00
69_I	73_R	0.759	1.00
89_T	207_S	0.756	1.00
91_Y	123_G	0.755	1.00
18_I	122_T	0.754	1.00
25_I	29_L	0.749	1.00
18_I	118_G	0.745	1.00
72_Y	76_N	0.741	1.00
183_G	202_M	0.740	1.00
43_E	46_L	0.736	1.00
182_A	209_L	0.733	1.00
156_S	160_E	0.729	1.00
6_V	160_E	0.728	1.00
133_T	136_D	0.727	1.00
147_V	170_D	0.727	1.00
91_Y	126_E	0.727	1.00
186_W	206_M	0.727	1.00
27_S	31_T	0.719	1.00
203_L	206_M	0.715	1.00
29_L	42_R	0.715	1.00
7_T	103_T	0.712	1.00
146_P	150_A	0.712	1.00
164_V	209_L	0.706	1.00
163_M	170_D	0.703	1.00
16_T	170_D	0.700	1.00
109_T	140_A	0.695	1.00
136_D	153_Q	0.690	1.00
92_E	96_A	0.690	1.00
14_D	118_G	0.688	1.00
144_P	176_N	0.684	1.00
54_F	66_E	0.681	1.00
184_V	206_M	0.681	1.00
109_T	142_P	0.679	1.00
119_L	125_G	0.673	1.00
10_L	105_G	0.673	1.00
44_D	47_A	0.672	1.00
24_I	28_F	0.671	1.00
70_A	73_R	0.670	1.00
19_N	85_T	0.668	1.00
171_V	183_G	0.668	1.00
46_L	49_I	0.658	1.00
104_L	129_E	0.657	1.00
107_V	163_M	0.657	1.00
172_L	175_K	0.656	1.00
7_T	156_S	0.654	1.00
73_R	77_H	0.654	1.00
22_E	85_T	0.649	1.00
158_P	161_A	0.647	1.00
132_V	146_P	0.646	1.00
68_M	72_Y	0.646	1.00
90_V	94_L	0.642	1.00
116_N	131_V	0.637	1.00
23_L	84_V	0.634	1.00
98_K	126_E	0.634	1.00
24_I	72_Y	0.631	1.00
68_M	71_M	0.630	1.00
15_G	21_N	0.628	1.00
86_E	122_T	0.627	1.00
115_V	131_V	0.625	1.00
18_I	84_V	0.622	1.00
89_T	93_T	0.622	1.00
130_T	150_A	0.620	1.00
98_K	101_G	0.615	1.00
35_Y	67_D	0.615	1.00
151_L	156_S	0.612	1.00
93_T	164_V	0.611	1.00
44_D	49_I	0.610	1.00
65_C	69_I	0.609	1.00
27_S	75_Y	0.607	1.00
146_P	173_A	0.606	1.00
49_I	52_S	0.604	1.00
151_L	177_A	0.598	1.00
11_F	93_T	0.597	1.00
33_E	38_S	0.597	1.00
16_T	184_V	0.594	1.00
56_T	60_M	0.594	1.00
67_D	70_A	0.594	1.00
40_Y	45_V	0.593	1.00
65_C	68_M	0.591	1.00
137_V	146_P	0.589	1.00
89_T	186_W	0.589	1.00
109_T	169_H	0.588	1.00
134_L	146_P	0.588	1.00
103_T	156_S	0.587	1.00
24_I	110_K	0.586	1.00
95_D	98_K	0.585	1.00
19_N	87_Y	0.584	1.00
163_M	173_A	0.583	1.00
10_L	147_V	0.580	1.00
107_V	132_V	0.580	1.00
119_L	124_I	0.578	1.00
19_N	22_E	0.578	1.00
120_K	126_E	0.572	1.00
128_F	131_V	0.571	1.00
20_T	110_K	0.567	1.00
22_E	26_A	0.567	1.00
148_L	151_L	0.563	1.00
81_D	117_M	0.560	1.00
151_L	157_E	0.557	1.00
93_T	97_L	0.555	1.00
115_V	119_L	0.553	1.00
88_E	207_S	0.552	1.00
77_H	117_M	0.552	1.00
44_D	48_F	0.550	1.00
28_F	32_L	0.549	1.00
113_D	117_M	0.549	1.00
183_G	199_P	0.544	1.00
51_P	55_D	0.543	1.00
110_K	165_G	0.539	1.00
56_T	59_S	0.539	1.00
93_T	203_L	0.532	1.00
110_K	114_T	0.528	1.00
52_S	55_D	0.525	1.00
25_I	45_V	0.524	1.00
109_T	134_L	0.521	1.00
20_T	24_I	0.520	1.00
168_Y	183_G	0.519	1.00
25_I	42_R	0.518	1.00
90_V	93_T	0.518	1.00
93_T	96_A	0.517	1.00
45_V	49_I	0.513	1.00
113_D	116_N	0.512	1.00
17_L	94_L	0.509	1.00
9_I	104_L	0.509	1.00
74_A	77_H	0.507	1.00
79_M	83_L	0.503	1.00
147_V	174_G	0.502	1.00
6_V	9_I	0.502	1.00
72_Y	75_Y	0.501	1.00
109_T	167_N	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
1swvA	2	0.9769	100	0.261	Contact Map
3d6jA	1	0.9537	100	0.267	Contact Map
4uw9A	1	0.9074	100	0.267	Contact Map
3sd7A	1	0.9769	100	0.267	Contact Map
3s6jA	2	0.9722	100	0.268	Contact Map
3iruA	4	0.9954	100	0.268	Contact Map
4eekA	2	0.9861	100	0.271	Contact Map
2hszA	1	0.9861	100	0.271	Contact Map
1te2A	2	0.9769	100	0.273	Contact Map
2hdoA	1	0.9491	100	0.275	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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