AROL - ECOLI - GREMLIN Contacts

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AROL - Shikimate kinase 2

UniProt:	P0A6E1	Sequences: MTQPLFLIGPRGCGKTTVGMALADSLNRRFVDTDQWLQSQLNMTVAEIVEREEWAGFRARETAALEAVTAPSTVIATGGGIILTEFNRHFMQNNGIVVYLCAPVSVLVNRLQAAPEEDLRPTLTGKPLSEEVQEVLEERDALYREVAHIIIDATNEPSQVISEIRSALAQTINC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10082
Length:	174 (159)
Sequences:	9763 (6741)
Seq/√Len:	534.6

ECOLI - AROL AROK KAD
BACSU - AROK KAD YQAC
HALSA - KAD KCY KAD6 Y2452
SULSO - KCY KAD6 Y1041

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_Q	67_A	2.952	1.00
104_V	136_L	2.797	1.00
25_S	165_R	2.692	1.00
133_Q	137_E	2.557	1.00
101_C	152_D	2.395	1.00
47_E	51_R	2.372	1.00
101_C	150_I	2.336	1.00
37_L	61_E	2.287	1.00
134_E	138_E	2.275	1.00
45_V	48_I	2.269	1.00
21_A	161_I	2.167	1.00
106_V	109_N	2.088	1.00
36_W	39_S	2.037	1.00
19_G	30_F	1.965	1.00
25_S	161_I	1.915	1.00
46_A	50_E	1.849	1.00
43_M	52_E	1.792	1.00
108_V	129_S	1.769	1.00
85_E	89_H	1.753	1.00
150_I	153_A	1.751	1.00
136_L	140_D	1.677	1.00
156_E	159_Q	1.663	1.00
62_T	90_F	1.651	1.00
62_T	86_F	1.623	1.00
6_F	95_G	1.552	1.00
43_M	51_R	1.540	1.00
62_T	84_T	1.516	1.00
144_R	150_I	1.492	1.00
130_E	134_E	1.485	1.00
59_A	63_A	1.452	1.00
36_W	64_A	1.435	1.00
26_L	165_R	1.426	1.00
111_L	128_L	1.421	1.00
18_V	164_I	1.384	1.00
13_C	102_A	1.379	1.00
49_V	57_F	1.378	1.00
52_E	56_G	1.375	1.00
103_P	154_T	1.374	1.00
62_T	81_I	1.370	1.00
104_V	133_Q	1.361	1.00
161_I	165_R	1.359	1.00
56_G	60_R	1.350	1.00
33_T	81_I	1.346	1.00
121_P	124_T	1.346	1.00
39_S	43_M	1.325	1.00
45_V	49_V	1.323	1.00
21_A	24_D	1.315	1.00
28_R	72_S	1.305	1.00
59_A	84_T	1.302	1.00
33_T	65_L	1.295	1.00
142_L	145_E	1.288	1.00
7_L	19_G	1.283	1.00
47_E	50_E	1.280	1.00
132_V	136_L	1.280	1.00
44_T	47_E	1.270	1.00
140_D	144_R	1.257	1.00
104_V	129_S	1.231	1.00
102_A	153_A	1.206	1.00
90_F	93_N	1.198	1.00
88_R	145_E	1.198	1.00
130_E	133_Q	1.169	1.00
18_V	161_I	1.161	1.00
129_S	133_Q	1.149	1.00
62_T	87_N	1.147	1.00
100_L	153_A	1.145	1.00
98_V	164_I	1.136	1.00
40_Q	64_A	1.134	1.00
56_G	59_A	1.133	1.00
31_V	73_T	1.131	1.00
23_A	30_F	1.127	1.00
66_E	70_A	1.122	1.00
21_A	158_S	1.120	1.00
46_A	49_V	1.102	1.00
10_P	135_V	1.097	1.00
18_V	160_V	1.093	1.00
83_L	142_L	1.082	1.00
48_I	52_E	1.078	1.00
108_V	112_Q	1.077	1.00
125_G	129_S	1.076	1.00
60_R	63_A	1.075	1.00
54_W	130_E	1.067	1.00
35_Q	38_Q	1.064	1.00
162_S	166_S	1.059	1.00
63_A	66_E	1.054	1.00
127_P	130_E	1.039	1.00
102_A	107_L	1.038	1.00
41_L	60_R	1.033	1.00
92_Q	148_H	1.024	1.00
124_T	127_P	1.020	1.00
113_A	116_E	1.020	1.00
163_E	167_A	1.007	1.00
48_I	57_F	1.000	1.00
36_W	40_Q	0.997	1.00
86_F	89_H	0.989	1.00
41_L	56_G	0.979	1.00
7_L	22_L	0.974	1.00
89_H	93_N	0.958	1.00
83_L	138_E	0.950	1.00
4_P	72_S	0.947	1.00
98_V	149_I	0.941	1.00
103_P	106_V	0.935	1.00
134_E	137_E	0.932	1.00
155_N	163_E	0.926	1.00
20_M	24_D	0.919	1.00
89_H	92_Q	0.909	1.00
4_P	73_T	0.908	1.00
162_S	165_R	0.903	1.00
126_K	131_E	0.900	1.00
66_E	94_N	0.890	1.00
49_V	54_W	0.888	1.00
102_A	106_V	0.885	1.00
100_L	164_I	0.881	1.00
82_I	142_L	0.880	1.00
149_I	167_A	0.872	1.00
112_Q	125_G	0.869	1.00
102_A	110_R	0.863	1.00
135_V	139_R	0.859	1.00
147_A	150_I	0.859	1.00
99_Y	140_D	0.859	1.00
131_E	134_E	0.859	1.00
55_A	59_A	0.852	1.00
10_P	107_L	0.851	1.00
38_Q	44_T	0.845	1.00
29_R	68_V	0.844	1.00
30_F	76_A	0.843	1.00
113_A	117_E	0.838	1.00
6_F	75_I	0.836	1.00
105_S	109_N	0.836	1.00
21_A	25_S	0.832	1.00
45_V	50_E	0.826	1.00
159_Q	163_E	0.819	1.00
152_D	155_N	0.816	1.00
157_P	161_I	0.811	1.00
65_L	81_I	0.810	1.00
91_M	97_V	0.810	1.00
88_R	142_L	0.807	1.00
35_Q	39_S	0.801	1.00
113_A	118_D	0.801	1.00
163_E	166_S	0.786	1.00
55_A	84_T	0.780	1.00
10_P	132_V	0.780	1.00
155_N	159_Q	0.780	1.00
40_Q	43_M	0.779	1.00
8_I	97_V	0.771	1.00
107_L	132_V	0.770	1.00
20_M	30_F	0.769	1.00
28_R	73_T	0.768	1.00
101_C	140_D	0.757	1.00
33_T	68_V	0.749	1.00
57_F	60_R	0.749	1.00
22_L	164_I	0.743	1.00
99_Y	150_I	0.742	1.00
45_V	63_A	0.736	1.00
104_V	108_V	0.733	1.00
6_F	91_M	0.732	1.00
4_P	28_R	0.730	1.00
106_V	154_T	0.725	1.00
25_S	162_S	0.723	1.00
125_G	128_L	0.722	1.00
91_M	95_G	0.717	1.00
62_T	65_L	0.711	1.00
84_T	87_N	0.707	1.00
62_T	66_E	0.703	1.00
116_E	119_L	0.698	1.00
44_T	48_I	0.697	1.00
17_T	157_P	0.695	1.00
149_I	153_A	0.694	1.00
66_E	90_F	0.692	1.00
104_V	132_V	0.689	1.00
92_Q	147_A	0.684	1.00
31_V	36_W	0.682	1.00
16_T	20_M	0.677	1.00
57_F	61_E	0.675	1.00
33_T	64_A	0.675	1.00
150_I	154_T	0.669	1.00
21_A	157_P	0.669	1.00
41_L	50_E	0.668	1.00
20_M	23_A	0.668	1.00
143_Y	148_H	0.666	1.00
12_G	111_L	0.660	1.00
105_S	129_S	0.652	1.00
18_V	157_P	0.646	1.00
32_D	76_A	0.646	1.00
92_Q	95_G	0.646	1.00
151_I	160_V	0.641	1.00
19_G	23_A	0.634	1.00
40_Q	63_A	0.633	1.00
22_L	161_I	0.629	1.00
41_L	48_I	0.627	1.00
48_I	54_W	0.626	1.00
48_I	56_G	0.624	1.00
85_E	88_R	0.621	1.00
99_Y	152_D	0.621	1.00
46_A	119_L	0.615	1.00
148_H	153_A	0.615	1.00
6_F	94_N	0.614	1.00
68_V	75_I	0.608	1.00
112_Q	124_T	0.604	1.00
96_I	168_L	0.604	1.00
8_I	99_Y	0.604	1.00
99_Y	144_R	0.597	1.00
96_I	149_I	0.595	1.00
13_C	99_Y	0.592	1.00
159_Q	162_S	0.590	0.99
36_W	67_A	0.589	0.99
131_E	135_V	0.584	0.99
23_A	74_V	0.579	0.99
11_R	122_T	0.576	0.99
118_D	124_T	0.574	0.99
22_L	74_V	0.572	0.99
4_P	71_P	0.567	0.99
14_G	17_T	0.563	0.99
125_G	131_E	0.558	0.99
33_T	36_W	0.556	0.99
108_V	128_L	0.551	0.99
31_V	68_V	0.551	0.99
101_C	144_R	0.548	0.99
7_L	74_V	0.547	0.99
92_Q	142_L	0.545	0.99
108_V	125_G	0.545	0.99
10_P	104_V	0.543	0.99
110_R	153_A	0.541	0.99
36_W	68_V	0.539	0.99
34_D	38_Q	0.533	0.99
7_L	100_L	0.530	0.99
13_C	100_L	0.526	0.99
61_E	65_L	0.525	0.99
106_V	155_N	0.520	0.99
65_L	87_N	0.520	0.99
152_D	163_E	0.519	0.99
43_M	47_E	0.518	0.99
11_R	49_V	0.518	0.99
143_Y	147_A	0.516	0.99
136_L	139_R	0.511	0.99
60_R	64_A	0.506	0.98
16_T	76_A	0.503	0.98
6_F	69_T	0.502	0.98
128_L	131_E	0.500	0.98

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
1e6cA	1	0.977	99.9	0.439	Contact Map
3gmtA	1	0.8391	99.9	0.443	Contact Map
4qbgB	1	0.9598	99.9	0.445	Contact Map
3cm0A	1	0.9425	99.9	0.447	Contact Map
4pzlA	2	0.9598	99.9	0.448	Contact Map
4jzkA	1	0.9368	99.9	0.45	Contact Map
1ukzA	1	0.9655	99.9	0.455	Contact Map
1zakA	2	0.977	99.9	0.456	Contact Map
2c95A	1	0.9713	99.9	0.457	Contact Map
3be4A	1	0.9425	99.9	0.464	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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