YJBM - BACSU - GREMLIN Contacts

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YJBM - GTP pyrophosphokinase YjbM

UniProt:	O31611	Sequences: MDDKQWERFLVPYRQAVEELKVKLKGIRTLYEYEDDHSPIEFVTGRVKPVASILEKARRKSIPLHEIETMQDIAGLRIMCQFVDDIQIVKEMLFARKDFTVVDQRDYIAEHKESGYRSYHLVVLYPLQTVSGEKHVLVEIQIRTLAMNFWATIEHSLNYKYSGNIPEKVKLRLQRASEAASRLDEEMSEIRGEVQEAQAAFSRKKKGSEQQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	211 (180)
Sequences:	5146 (3183)
Seq/√Len:	237.2

ECOLI - RELA SPOT
BACSU - YJBM YWAC 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
82_F	85_D	3.616	1.00
81_Q	145_L	3.279	1.00
79_M	145_L	2.675	1.00
44_T	148_N	2.543	1.00
55_E	59_R	2.529	1.00
28_R	32_E	2.518	1.00
85_D	88_I	2.467	1.00
42_F	145_L	2.443	1.00
34_E	37_H	2.439	1.00
100_T	124_L	2.330	1.00
5_Q	8_R	2.300	1.00
8_R	12_P	2.213	1.00
41_E	81_Q	2.153	1.00
80_C	89_V	2.149	1.00
94_F	104_Q	2.084	1.00
174_Q	178_E	2.051	1.00
17_V	47_V	1.992	1.00
21_K	25_K	1.982	1.00
31_Y	93_L	1.970	1.00
12_P	67_I	1.943	1.00
17_V	21_K	1.837	1.00
186_E	191_R	1.836	1.00
34_E	96_R	1.835	1.00
7_E	10_L	1.831	1.00
123_V	140_I	1.820	1.00
81_Q	85_D	1.807	1.00
84_D	88_I	1.794	1.00
27_I	138_V	1.753	1.00
90_K	94_F	1.726	1.00
22_V	26_G	1.709	1.00
118_S	143_R	1.671	1.00
124_L	135_H	1.652	1.00
10_L	50_V	1.646	1.00
87_Q	109_A	1.619	1.00
11_V	15_Q	1.574	1.00
26_G	134_K	1.571	1.00
187_M	191_R	1.548	1.00
62_I	70_M	1.528	1.00
94_F	121_L	1.523	1.00
90_K	104_Q	1.482	1.00
29_T	33_Y	1.473	1.00
90_K	119_Y	1.473	1.00
145_L	149_F	1.467	1.00
71_Q	137_L	1.464	1.00
167_E	171_L	1.446	1.00
175_R	179_A	1.442	1.00
63_P	68_E	1.438	1.00
87_Q	91_E	1.426	1.00
148_N	152_T	1.425	1.00
35_D	89_V	1.421	1.00
54_L	58_R	1.411	1.00
170_K	177_S	1.390	1.00
16_A	19_E	1.379	1.00
13_Y	50_V	1.372	1.00
62_I	69_T	1.370	1.00
90_K	121_L	1.354	1.00
174_Q	177_S	1.344	1.00
53_I	70_M	1.342	1.00
169_V	179_A	1.333	1.00
9_F	50_V	1.315	1.00
32_E	36_D	1.313	1.00
15_Q	136_V	1.289	1.00
33_Y	37_H	1.287	1.00
168_K	171_L	1.279	1.00
169_V	175_R	1.274	1.00
52_S	160_K	1.262	1.00
91_E	94_F	1.251	1.00
93_L	140_I	1.249	1.00
7_E	11_V	1.238	1.00
25_K	28_R	1.233	1.00
175_R	182_R	1.222	1.00
172_R	186_E	1.215	1.00
34_E	92_M	1.205	1.00
174_Q	181_S	1.202	1.00
30_L	97_K	1.193	1.00
29_T	32_E	1.182	1.00
93_L	123_V	1.168	1.00
123_V	138_V	1.163	1.00
87_Q	106_D	1.153	1.00
117_R	150_W	1.138	1.00
89_V	92_M	1.134	1.00
51_A	55_E	1.122	1.00
103_D	122_V	1.120	1.00
10_L	14_R	1.110	1.00
158_N	170_K	1.092	1.00
46_R	75_G	1.082	1.00
77_R	141_Q	1.070	1.00
94_F	101_V	1.069	1.00
172_R	178_E	1.047	1.00
169_V	177_S	1.044	1.00
23_K	125_Y	1.043	1.00
6_W	10_L	1.042	1.00
146_A	149_F	1.019	1.00
11_V	14_R	1.019	1.00
182_R	186_E	1.015	1.00
14_R	29_T	1.012	1.00
24_L	45_G	1.006	1.00
167_E	170_K	1.000	1.00
34_E	38_S	0.985	1.00
30_L	96_R	0.982	1.00
188_S	192_G	0.981	1.00
170_K	175_R	0.979	1.00
32_E	42_F	0.974	1.00
18_E	21_K	0.960	1.00
124_L	137_L	0.958	1.00
48_K	141_Q	0.951	1.00
26_G	30_L	0.950	1.00
38_S	92_M	0.933	1.00
105_R	122_V	0.914	1.00
77_R	143_R	0.914	1.00
169_V	173_L	0.912	1.00
27_I	76_L	0.911	1.00
169_V	176_A	0.907	1.00
31_Y	140_I	0.904	1.00
170_K	179_A	0.900	1.00
88_I	91_E	0.896	1.00
100_T	104_Q	0.892	0.99
107_Y	112_K	0.885	0.99
116_Y	120_H	0.868	0.99
48_K	77_R	0.868	0.99
115_G	150_W	0.862	0.99
46_R	160_K	0.857	0.99
175_R	181_S	0.853	0.99
104_Q	121_L	0.843	0.99
48_K	75_G	0.833	0.99
171_L	174_Q	0.832	0.99
78_I	142_I	0.829	0.99
80_C	85_D	0.824	0.99
25_K	29_T	0.811	0.99
174_Q	179_A	0.807	0.99
74_A	138_V	0.806	0.99
170_K	174_Q	0.793	0.99
168_K	172_R	0.784	0.99
172_R	179_A	0.783	0.99
176_A	179_A	0.783	0.99
88_I	92_M	0.778	0.99
186_E	190_I	0.777	0.99
56_K	141_Q	0.767	0.98
179_A	183_L	0.761	0.98
18_E	25_K	0.760	0.98
26_G	29_T	0.760	0.98
48_K	56_K	0.759	0.98
23_K	74_A	0.750	0.98
186_E	193_E	0.748	0.98
9_F	12_P	0.746	0.98
48_K	139_E	0.743	0.98
169_V	172_R	0.740	0.98
107_Y	117_R	0.734	0.98
46_R	159_Y	0.730	0.98
30_L	34_E	0.729	0.98
185_E	189_E	0.729	0.98
56_K	75_G	0.729	0.98
172_R	182_R	0.729	0.98
180_A	183_L	0.729	0.98
48_K	72_D	0.723	0.98
4_K	7_E	0.715	0.98
47_V	50_V	0.714	0.98
56_K	139_E	0.711	0.98
175_R	180_A	0.707	0.97
177_S	180_A	0.705	0.97
169_V	184_D	0.700	0.97
188_S	191_R	0.700	0.97
52_S	118_S	0.699	0.97
16_A	20_L	0.698	0.97
114_S	147_M	0.697	0.97
74_A	136_V	0.694	0.97
46_R	139_E	0.693	0.97
12_P	16_A	0.692	0.97
72_D	141_Q	0.691	0.97
87_Q	108_I	0.690	0.97
56_K	159_Y	0.685	0.97
175_R	186_E	0.683	0.97
28_R	76_L	0.681	0.97
187_M	190_I	0.680	0.97
146_A	150_W	0.672	0.96
57_A	62_I	0.671	0.96
81_Q	156_S	0.671	0.96
172_R	175_R	0.670	0.96
172_R	193_E	0.669	0.96
87_Q	94_F	0.665	0.96
169_V	174_Q	0.664	0.96
99_F	109_A	0.663	0.96
89_V	142_I	0.659	0.96
56_K	77_R	0.658	0.96
52_S	151_A	0.657	0.96
15_Q	134_K	0.654	0.96
20_L	47_V	0.651	0.96
59_R	62_I	0.650	0.96
75_G	141_Q	0.649	0.96
85_D	89_V	0.641	0.95
56_K	160_K	0.640	0.95
77_R	159_Y	0.639	0.95
156_S	159_Y	0.639	0.95
24_L	47_V	0.636	0.95
91_E	95_A	0.634	0.95
77_R	139_E	0.634	0.95
169_V	180_A	0.630	0.95
175_R	183_L	0.629	0.95
178_E	182_R	0.629	0.95
170_K	182_R	0.628	0.95
172_R	180_A	0.627	0.95
87_Q	107_Y	0.626	0.95
23_K	27_I	0.625	0.95
55_E	58_R	0.624	0.95
86_I	119_Y	0.620	0.95
91_E	109_A	0.617	0.94
122_V	137_L	0.615	0.94
107_Y	111_H	0.612	0.94
63_P	69_T	0.612	0.94
183_L	187_M	0.607	0.94
75_G	159_Y	0.605	0.94
98_D	110_E	0.605	0.94
70_M	137_L	0.595	0.93
28_R	45_G	0.594	0.93
78_I	89_V	0.594	0.93
185_E	191_R	0.593	0.93
72_D	77_R	0.589	0.93
87_Q	119_Y	0.588	0.93
56_K	72_D	0.588	0.93
167_E	177_S	0.587	0.93
111_H	119_Y	0.586	0.93
72_D	75_G	0.585	0.93
86_I	142_I	0.584	0.93
126_P	134_K	0.583	0.93
4_K	8_R	0.583	0.93
176_A	182_R	0.576	0.92
189_E	192_G	0.575	0.92
74_A	122_V	0.573	0.92
38_S	88_I	0.568	0.92
28_R	43_V	0.568	0.92
51_A	54_L	0.568	0.92
86_I	90_K	0.566	0.91
23_K	138_V	0.565	0.91
13_Y	53_I	0.563	0.91
42_F	148_N	0.556	0.91
61_S	134_K	0.554	0.91
27_I	137_L	0.552	0.90
102_V	137_L	0.552	0.90
19_E	22_V	0.551	0.90
92_M	95_A	0.546	0.90
30_L	33_Y	0.545	0.90
172_R	176_A	0.545	0.90
8_R	11_V	0.542	0.90
183_L	186_E	0.540	0.89
80_C	83_V	0.540	0.89
36_D	41_E	0.535	0.89
175_R	178_E	0.535	0.89
86_I	108_I	0.532	0.89
9_F	53_I	0.531	0.89
121_L	142_I	0.531	0.89
17_V	50_V	0.530	0.89
87_Q	90_K	0.529	0.88
21_K	123_V	0.527	0.88
57_A	60_K	0.525	0.88
83_V	117_R	0.524	0.88
108_I	114_S	0.519	0.88
139_E	159_Y	0.518	0.87
15_Q	19_E	0.517	0.87
150_W	190_I	0.514	0.87
8_R	58_R	0.513	0.87
186_E	189_E	0.512	0.87
86_I	147_M	0.512	0.87
28_R	44_T	0.511	0.87
106_D	109_A	0.511	0.87
164_N	168_K	0.506	0.86
146_A	180_A	0.505	0.86
46_R	56_K	0.502	0.86
44_T	152_T	0.502	0.86
181_S	185_E	0.500	0.86
98_D	124_L	0.500	0.86

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
3l9dA	1	0.9289	100	0.215	Contact Map
1vj7A	1	0.7251	100	0.216	Contact Map
2be3A	2	0.9479	100	0.22	Contact Map
3f9tA	2	0.4313	12	0.951	Contact Map
3k40A	2	0.4834	11.6	0.951	Contact Map
2dgkA	3	0.5498	11.4	0.951	Contact Map
3j3wN	1	0.5498	10.6	0.952	Contact Map
3getA	2	0.4408	9.4	0.953	Contact Map
3u1kA	3	0.4265	8.9	0.954	Contact Map
1fg7A	2	0.455	8.5	0.954	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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