YWAC - BACSU - GREMLIN Contacts

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YWAC - GTP pyrophosphokinase YwaC

UniProt:	P39583	Sequences: MDLSVTHMDDLKTVMEDWKNELLVYKFALDALDTKFSIISQEYNLIHGHNPIEHTKSRVKSFESIVNKLMRKGCEITTKEMKEHIHDIAGVRIICSFISDIYNVVNVLKQHEDLRIVKVKDYIQTPKPNGYRSLHLIIEMPVNLTNRVEYVKAEIQIRTIAMDFWASLEHKIYYKLNNDVPKQLTDELKEAAEIAHYLDEKMLGIKKEVD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	210 (180)
Sequences:	5167 (3159)
Seq/√Len:	235.4

ECOLI - RELA SPOT
BACSU - YWAC YJBM RELA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_F	100_D	3.678	1.00
96_S	160_I	3.207	1.00
14_V	17_D	2.795	1.00
67_N	71_R	2.708	1.00
56_K	163_D	2.675	1.00
94_I	160_I	2.551	1.00
54_H	160_I	2.515	1.00
100_D	103_N	2.511	1.00
115_R	139_E	2.472	1.00
40_S	44_N	2.469	1.00
46_I	49_H	2.326	1.00
53_E	96_S	2.217	1.00
20_N	24_V	2.192	1.00
95_C	104_V	2.157	1.00
109_K	119_V	2.107	1.00
29_L	59_V	2.100	1.00
17_D	20_N	2.096	1.00
189_K	193_E	2.051	1.00
43_Y	108_L	2.035	1.00
46_I	111_H	1.972	1.00
138_I	155_I	1.934	1.00
102_Y	124_Q	1.790	1.00
105_V	109_K	1.786	1.00
19_K	22_L	1.783	1.00
187_E	201_K	1.780	1.00
139_E	150_Y	1.778	1.00
133_S	158_R	1.777	1.00
33_D	37_S	1.724	1.00
96_S	100_D	1.719	1.00
22_L	62_F	1.709	1.00
39_I	153_A	1.696	1.00
29_L	33_D	1.677	1.00
34_T	38_I	1.673	1.00
99_S	103_N	1.654	1.00
86_H	152_K	1.599	1.00
105_V	134_L	1.580	1.00
74_C	85_I	1.563	1.00
74_C	84_H	1.558	1.00
38_I	149_E	1.552	1.00
160_I	164_F	1.551	1.00
109_K	136_L	1.530	1.00
28_A	31_A	1.528	1.00
108_L	155_I	1.490	1.00
105_V	119_V	1.443	1.00
65_I	85_I	1.434	1.00
75_E	83_E	1.430	1.00
23_L	27_F	1.410	1.00
187_E	190_E	1.370	1.00
21_E	62_F	1.368	1.00
163_D	167_S	1.367	1.00
105_V	136_L	1.365	1.00
190_E	197_Y	1.328	1.00
25_Y	62_F	1.310	1.00
45_L	49_H	1.286	1.00
24_V	76_I	1.285	1.00
44_N	48_G	1.282	1.00
102_Y	106_N	1.276	1.00
41_Q	45_L	1.267	1.00
66_V	70_M	1.258	1.00
64_S	175_K	1.258	1.00
173_Y	185_T	1.255	1.00
104_V	107_V	1.240	1.00
138_I	153_A	1.238	1.00
27_F	151_V	1.236	1.00
37_S	40_S	1.230	1.00
41_Q	44_N	1.223	1.00
106_N	109_K	1.208	1.00
182_K	186_D	1.181	1.00
10_D	14_V	1.177	1.00
132_R	165_W	1.175	1.00
197_Y	201_K	1.173	1.00
47_H	104_V	1.161	1.00
92_R	156_Q	1.159	1.00
63_E	67_N	1.150	1.00
108_L	138_I	1.142	1.00
109_K	116_I	1.140	1.00
161_A	164_F	1.138	1.00
36_F	57_S	1.130	1.00
190_E	198_L	1.127	1.00
19_K	23_L	1.126	1.00
9_D	12_K	1.121	1.00
42_E	112_E	1.119	1.00
118_K	137_I	1.112	1.00
182_K	185_T	1.111	1.00
46_I	107_V	1.104	1.00
22_L	26_K	1.088	1.00
35_K	140_M	1.085	1.00
11_L	22_L	1.069	1.00
60_K	156_Q	1.056	1.00
195_A	198_L	1.054	1.00
58_R	90_G	1.049	1.00
183_Q	186_D	1.042	1.00
190_E	201_K	1.035	1.00
102_Y	121_D	1.029	1.00
119_V	136_L	1.028	1.00
43_Y	155_I	1.008	1.00
92_R	158_R	0.992	1.00
46_I	50_N	0.974	1.00
193_E	197_Y	0.970	1.00
95_C	100_D	0.969	1.00
139_E	152_K	0.945	1.00
15_M	19_K	0.937	1.00
187_E	197_Y	0.931	1.00
60_K	68_K	0.927	1.00
60_K	90_G	0.924	1.00
44_N	54_H	0.923	1.00
185_T	192_A	0.919	1.00
30_D	33_D	0.910	1.00
23_L	26_K	0.909	1.00
190_E	194_I	0.906	1.00
38_I	42_E	0.900	1.00
26_K	41_Q	0.896	0.99
194_I	197_Y	0.895	0.99
115_R	119_V	0.894	0.99
18_W	22_L	0.894	0.99
103_N	106_N	0.883	0.99
189_K	192_A	0.880	0.99
60_K	92_R	0.876	0.99
186_D	189_K	0.876	0.99
130_G	165_W	0.874	0.99
89_A	151_V	0.865	0.99
39_I	91_V	0.859	0.99
102_Y	123_I	0.856	0.99
42_E	111_H	0.850	0.99
184_L	199_D	0.845	0.99
187_E	193_E	0.844	0.99
28_A	32_L	0.837	0.99
32_L	59_V	0.835	0.99
89_A	153_A	0.832	0.99
122_Y	127_K	0.828	0.99
35_K	89_A	0.828	0.99
129_N	162_M	0.827	0.99
10_D	17_D	0.823	0.99
21_E	24_V	0.817	0.99
64_S	133_S	0.817	0.99
194_I	198_L	0.814	0.99
120_K	137_I	0.811	0.99
59_V	62_F	0.810	0.99
68_K	156_Q	0.807	0.99
60_K	154_E	0.807	0.99
69_L	76_I	0.807	0.99
68_K	154_E	0.798	0.99
173_Y	192_A	0.791	0.99
101_I	123_I	0.781	0.99
48_G	53_E	0.779	0.99
192_A	195_A	0.776	0.99
58_R	175_K	0.768	0.98
96_S	171_K	0.768	0.98
40_S	91_V	0.763	0.98
104_V	157_I	0.754	0.98
60_K	87_D	0.746	0.98
93_I	157_I	0.745	0.98
114_L	124_Q	0.743	0.98
58_R	174_Y	0.742	0.98
42_E	46_I	0.742	0.98
64_S	166_A	0.741	0.98
21_E	65_I	0.740	0.98
90_G	156_Q	0.738	0.98
68_K	174_Y	0.737	0.98
37_S	41_Q	0.724	0.98
123_I	127_K	0.717	0.98
58_R	154_E	0.717	0.98
161_A	165_W	0.708	0.97
75_E	84_H	0.703	0.97
30_D	37_S	0.699	0.97
68_K	90_G	0.699	0.97
194_I	201_K	0.698	0.97
102_Y	109_K	0.695	0.97
121_D	126_P	0.686	0.97
184_L	188_L	0.686	0.97
68_K	92_R	0.684	0.97
21_E	69_L	0.683	0.97
35_K	141_P	0.681	0.97
181_P	184_L	0.680	0.97
102_Y	122_Y	0.680	0.97
122_Y	132_R	0.679	0.97
113_D	125_T	0.677	0.97
16_E	19_K	0.674	0.96
187_E	192_A	0.669	0.96
106_N	110_Q	0.668	0.96
122_Y	126_P	0.667	0.96
73_G	149_E	0.664	0.96
50_N	107_V	0.663	0.96
184_L	187_E	0.662	0.96
193_E	200_E	0.662	0.96
171_K	175_K	0.660	0.96
93_I	104_V	0.657	0.96
89_A	137_I	0.656	0.96
60_K	174_Y	0.654	0.96
25_Y	65_I	0.649	0.96
113_D	139_E	0.648	0.96
24_V	28_A	0.644	0.95
90_G	174_Y	0.642	0.95
36_F	59_V	0.640	0.95
29_L	62_F	0.640	0.95
38_I	41_Q	0.640	0.95
11_L	19_K	0.635	0.95
131_Y	135_H	0.634	0.95
137_I	152_K	0.632	0.95
87_D	156_Q	0.632	0.95
190_E	196_H	0.622	0.95
14_V	19_K	0.622	0.95
26_K	30_D	0.620	0.94
92_R	154_E	0.620	0.94
40_S	57_S	0.615	0.94
63_E	66_V	0.610	0.94
106_N	124_Q	0.602	0.94
92_R	174_Y	0.600	0.93
191_A	197_Y	0.595	0.93
40_S	55_T	0.594	0.93
141_P	149_E	0.594	0.93
171_K	174_Y	0.590	0.93
35_K	39_I	0.589	0.93
102_Y	134_L	0.588	0.93
86_H	118_K	0.587	0.93
154_E	174_Y	0.583	0.92
71_R	74_C	0.583	0.92
98_I	110_Q	0.581	0.92
39_I	152_K	0.578	0.92
87_D	90_G	0.578	0.92
169_E	172_I	0.574	0.92
87_D	92_R	0.574	0.92
103_N	107_V	0.572	0.92
102_Y	105_V	0.571	0.92
101_I	157_I	0.565	0.91
69_L	74_C	0.565	0.91
105_V	157_I	0.564	0.91
43_Y	47_H	0.563	0.91
27_F	31_A	0.561	0.91
36_F	91_V	0.561	0.91
191_A	195_A	0.557	0.91
10_D	62_F	0.556	0.91
123_I	129_N	0.556	0.91
165_W	188_L	0.554	0.90
98_I	132_R	0.548	0.90
36_F	89_A	0.547	0.90
188_L	192_A	0.546	0.90
56_K	167_S	0.545	0.90
68_K	175_K	0.545	0.90
187_E	194_I	0.545	0.90
67_N	70_M	0.541	0.89
188_L	199_D	0.540	0.89
168_L	172_I	0.539	0.89
121_D	129_N	0.534	0.89
98_I	159_T	0.533	0.89
136_L	157_I	0.531	0.88
191_A	194_I	0.529	0.88
65_I	88_I	0.529	0.88
197_Y	200_E	0.529	0.88
117_V	152_K	0.526	0.88
32_L	153_A	0.524	0.88
11_L	18_W	0.523	0.88
180_V	184_L	0.523	0.88
101_I	105_V	0.523	0.88
193_E	199_D	0.523	0.88
30_D	34_T	0.522	0.88
35_K	151_V	0.518	0.87
20_N	70_M	0.518	0.87
53_E	176_L	0.517	0.87
20_N	23_L	0.517	0.87
53_E	100_D	0.516	0.87
27_F	149_E	0.513	0.87
72_K	76_I	0.510	0.86
56_K	94_I	0.508	0.86
101_I	134_L	0.506	0.86
123_I	162_M	0.506	0.86
180_V	183_Q	0.503	0.86
107_V	110_Q	0.502	0.86
68_K	87_D	0.500	0.85
90_G	154_E	0.500	0.85

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
1vj7A	1	0.7857	100	0.189	Contact Map
3l9dA	1	0.9048	100	0.223	Contact Map
2be3A	2	0.9286	100	0.238	Contact Map
2dgkA	3	0.6238	12.1	0.951	Contact Map
3j3wN	1	0.5524	11.1	0.952	Contact Map
3d7aA	2	0.5286	11	0.952	Contact Map
4otnA	2	0.3667	10.9	0.953	Contact Map
1fg7A	2	0.519	7.5	0.956	Contact Map
3k66A	1	0.381	7.4	0.956	Contact Map
3f9tA	2	0.4905	7.2	0.956	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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