NUDK - ECOLI - GREMLIN Contacts

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NUDK - GDP-mannose pyrophosphatase NudK

UniProt:	P37128	Sequences: MTQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12410
Length:	191 (165)
Sequences:	5806 (4108)
Seq/√Len:	319.8

ECOLI - NUDK NUDE ADPP
BACSU - ADPP
HALSA - Q9HNS9 Q9HME6
SULSO - Q97WP3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_T	83_S	3.028	1.00
94_E	98_R	2.608	1.00
111_E	135_E	2.539	1.00
54_N	59_T	2.480	1.00
102_I	108_E	2.444	1.00
164_L	185_Q	2.392	1.00
59_T	159_P	2.352	1.00
163_A	181_L	2.284	1.00
59_T	157_E	2.281	1.00
81_I	156_L	2.191	1.00
22_N	38_K	2.189	1.00
14_S	19_T	2.181	1.00
113_R	135_E	2.152	1.00
165_E	169_T	2.112	1.00
24_T	36_R	2.095	1.00
114_K	130_H	2.087	1.00
92_E	95_V	2.087	1.00
61_V	157_E	2.070	1.00
64_R	154_E	2.032	1.00
117_E	128_L	1.967	1.00
21_H	43_D	1.966	1.00
26_D	36_R	1.965	1.00
8_I	24_T	1.965	1.00
88_L	96_C	1.922	1.00
91_D	99_K	1.908	1.00
43_D	126_T	1.905	1.00
54_N	157_E	1.896	1.00
114_K	117_E	1.861	1.00
166_M	171_E	1.859	1.00
11_K	14_S	1.854	1.00
64_R	156_L	1.819	1.00
98_R	112_V	1.809	1.00
50_I	97_I	1.788	1.00
158_L	166_M	1.705	1.00
65_Q	82_E	1.687	1.00
23_I	68_V	1.675	1.00
24_T	38_K	1.667	1.00
93_P	130_H	1.649	1.00
10_D	22_N	1.628	1.00
117_E	130_H	1.594	1.00
101_A	109_V	1.574	1.00
22_N	40_E	1.571	1.00
159_P	162_Q	1.549	1.00
162_Q	165_E	1.518	1.00
119_Y	173_R	1.498	1.00
94_E	112_V	1.489	1.00
51_L	180_L	1.479	1.00
95_V	98_R	1.472	1.00
83_S	180_L	1.458	1.00
27_L	31_D	1.455	1.00
96_C	99_K	1.443	1.00
78_G	173_R	1.441	1.00
54_N	57_K	1.420	1.00
9_K	23_I	1.356	1.00
61_V	107_Y	1.352	1.00
88_L	93_P	1.346	1.00
15_D	40_E	1.314	1.00
51_L	184_L	1.302	1.00
84_C	105_T	1.295	1.00
102_I	146_G	1.288	1.00
9_K	21_H	1.265	1.00
102_I	143_N	1.239	1.00
68_V	77_S	1.239	1.00
118_L	179_L	1.224	1.00
139_N	142_A	1.198	1.00
158_L	163_A	1.185	1.00
30_K	152_D	1.179	1.00
98_R	102_I	1.157	1.00
114_K	132_F	1.152	1.00
91_D	96_C	1.147	1.00
70_T	80_L	1.137	1.00
118_L	131_F	1.135	1.00
70_T	119_Y	1.129	1.00
46_N	88_L	1.121	1.00
52_L	101_A	1.118	1.00
93_P	132_F	1.112	1.00
61_V	155_V	1.108	1.00
121_S	127_E	1.073	1.00
165_E	168_K	1.070	1.00
164_L	168_K	1.051	1.00
23_I	41_V	1.027	1.00
162_Q	166_M	1.020	1.00
167_I	178_V	1.019	1.00
64_R	79_Q	0.991	1.00
115_L	133_I	0.985	1.00
110_G	139_N	0.975	1.00
141_R	144_A	0.963	1.00
48_A	97_I	0.949	1.00
58_K	160_F	0.946	1.00
109_V	112_V	0.933	1.00
145_G	148_V	0.929	1.00
18_F	42_Y	0.914	1.00
131_F	180_L	0.911	1.00
80_L	122_P	0.911	1.00
11_K	19_T	0.907	1.00
66_F	77_S	0.903	1.00
53_Y	133_I	0.901	1.00
7_L	26_D	0.887	1.00
94_E	114_K	0.878	1.00
44_R	127_E	0.869	1.00
179_L	182_N	0.866	1.00
60_V	83_S	0.864	1.00
47_G	129_I	0.855	1.00
49_T	129_I	0.855	1.00
51_L	60_V	0.850	1.00
107_Y	142_A	0.845	1.00
97_I	112_V	0.845	1.00
11_K	21_H	0.836	1.00
10_D	24_T	0.835	1.00
27_L	30_K	0.827	1.00
46_N	128_L	0.825	1.00
42_Y	124_G	0.821	1.00
67_R	82_E	0.817	1.00
60_V	181_L	0.815	1.00
109_V	134_A	0.811	1.00
50_I	134_A	0.811	1.00
41_V	68_V	0.808	1.00
110_G	140_Q	0.802	1.00
174_D	177_T	0.801	1.00
54_N	107_Y	0.795	1.00
70_T	78_G	0.790	1.00
53_Y	160_F	0.787	1.00
119_Y	128_L	0.771	1.00
51_L	83_S	0.769	1.00
46_N	130_H	0.758	0.99
60_V	184_L	0.757	0.99
164_L	181_L	0.755	0.99
83_S	181_L	0.749	0.99
49_T	176_K	0.748	0.99
108_E	142_A	0.747	0.99
98_R	108_E	0.745	0.99
20_L	42_Y	0.745	0.99
19_T	43_D	0.742	0.99
147_G	153_I	0.741	0.99
7_L	36_R	0.737	0.99
49_T	131_F	0.736	0.99
62_L	158_L	0.731	0.99
10_D	21_H	0.730	0.99
112_V	134_A	0.728	0.99
62_L	156_L	0.725	0.99
113_R	133_I	0.723	0.99
62_L	81_I	0.723	0.99
167_I	172_I	0.723	0.99
55_T	135_E	0.722	0.99
120_M	124_G	0.722	0.99
166_M	169_T	0.709	0.99
58_K	161_S	0.707	0.99
84_C	101_A	0.700	0.99
118_L	175_G	0.694	0.99
111_E	114_K	0.694	0.99
116_F	179_L	0.692	0.99
107_Y	141_R	0.692	0.99
53_Y	60_V	0.691	0.99
25_Y	37_H	0.688	0.99
31_D	152_D	0.682	0.99
172_I	177_T	0.681	0.99
129_I	176_K	0.676	0.99
79_Q	152_D	0.668	0.99
94_E	132_F	0.666	0.99
121_S	125_V	0.657	0.98
112_V	132_F	0.655	0.98
52_L	133_I	0.655	0.98
85_A	176_K	0.655	0.98
53_Y	58_K	0.655	0.98
81_I	158_L	0.649	0.98
52_L	63_I	0.647	0.98
110_G	141_R	0.646	0.98
63_I	153_I	0.644	0.98
62_L	163_A	0.637	0.98
163_A	167_I	0.637	0.98
48_A	93_P	0.636	0.98
13_L	17_Y	0.635	0.98
12_I	20_L	0.634	0.98
64_R	81_I	0.630	0.98
102_I	144_A	0.629	0.98
53_Y	135_E	0.627	0.98
60_V	160_F	0.624	0.98
116_F	183_Y	0.624	0.98
140_Q	143_N	0.620	0.98
97_I	132_F	0.617	0.98
85_A	123_G	0.616	0.98
128_L	173_R	0.610	0.97
139_N	143_N	0.610	0.97
116_F	170_G	0.610	0.97
8_I	36_R	0.609	0.97
10_D	38_K	0.607	0.97
15_D	19_T	0.599	0.97
117_E	173_R	0.597	0.97
8_I	26_D	0.595	0.97
167_I	181_L	0.589	0.97
182_N	185_Q	0.589	0.97
27_L	37_H	0.585	0.97
108_E	141_R	0.583	0.97
55_T	58_K	0.580	0.97
97_I	101_A	0.580	0.97
158_L	162_Q	0.577	0.97
120_M	175_G	0.577	0.97
47_G	87_L	0.576	0.96
179_L	183_Y	0.576	0.96
159_P	164_L	0.574	0.96
161_S	164_L	0.574	0.96
80_L	119_Y	0.573	0.96
45_G	87_L	0.573	0.96
60_V	163_A	0.573	0.96
81_I	166_M	0.569	0.96
111_E	139_N	0.566	0.96
49_T	85_A	0.566	0.96
120_M	125_V	0.565	0.96
16_N	22_N	0.564	0.96
160_F	164_L	0.563	0.96
46_N	87_L	0.562	0.96
156_L	166_M	0.562	0.96
12_I	15_D	0.562	0.96
52_L	109_V	0.561	0.96
178_V	182_N	0.561	0.96
118_L	178_V	0.557	0.96
166_M	172_I	0.549	0.95
67_R	123_G	0.548	0.95
108_E	140_Q	0.543	0.95
8_I	11_K	0.538	0.95
53_Y	184_L	0.538	0.95
52_L	83_S	0.536	0.95
143_N	146_G	0.535	0.95
20_L	40_E	0.532	0.95
16_N	40_E	0.532	0.95
181_L	185_Q	0.531	0.95
50_I	84_C	0.530	0.94
44_R	124_G	0.529	0.94
116_F	178_V	0.525	0.94
23_I	77_S	0.519	0.94
160_F	185_Q	0.518	0.94
88_L	130_H	0.517	0.94
26_D	33_E	0.516	0.94
13_L	20_L	0.516	0.94
92_E	132_F	0.516	0.94
141_R	145_G	0.515	0.94
14_S	22_N	0.515	0.94
145_G	155_V	0.514	0.94
25_Y	68_V	0.513	0.93
57_K	157_E	0.513	0.93
54_N	61_V	0.512	0.93
115_L	184_L	0.512	0.93
12_I	22_N	0.512	0.93
100_E	104_E	0.511	0.93
162_Q	171_E	0.508	0.93
143_N	147_G	0.506	0.93
133_I	183_Y	0.503	0.93
140_Q	144_A	0.500	0.93

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
1g0sA	2	0.9895	100	0.334	Contact Map
2dscA	2	0.9215	100	0.353	Contact Map
1vhzA	2	0.9215	100	0.363	Contact Map
3o6zA	2	0.9948	100	0.376	Contact Map
1mk1A	2	0.8429	100	0.405	Contact Map
2yvpA	2	0.9162	100	0.438	Contact Map
3q91A	2	0.7173	99.9	0.486	Contact Map
1v8yA	2	0.7749	99.9	0.492	Contact Map
2w4eA	2	0.6963	99.9	0.561	Contact Map
2fvvA	1	0.7016	99.8	0.605	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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