NUDL - ECOLI - GREMLIN Contacts

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NUDL - Uncharacterized Nudix hydrolase NudL

UniProt:	P43337	Sequences: MEYRSLTLDDFLSRFQLLRPQINRETLNHRQAAVLIPIVRRPQPGLLLTQRSIHLRKHAGQVAFPGGAVDDTDASAIAAALREAEEEVAIPPSAVEVIGVLPPVDSVTGYQVTPVVGIIPPDLPYRASEDEVSAVFEMPLAQALHLGRYHPLDIYRRGDSHRVWLSWYEQYFVWGMTAGIIRELALQIGVKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12693
Length:	192 (167)
Sequences:	3101 (2295)
Seq/√Len:	177.6

ECOLI - NUDL
HALSA - Q9HSE2
SULSO - Q97U56

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_V	79_A	5.227	1.00
48_L	181_I	3.570	1.00
77_I	115_V	2.914	1.00
85_E	92_P	2.724	1.00
95_V	117_G	2.677	1.00
74_A	78_A	2.672	1.00
35_L	84_A	2.546	1.00
43_Q	141_A	2.445	1.00
49_T	63_A	2.350	1.00
69_V	76_A	2.310	1.00
134_A	171_Y	2.275	1.00
127_A	135_V	2.267	1.00
75_S	78_A	2.222	1.00
45_G	137_E	2.155	1.00
35_L	117_G	2.128	1.00
96_E	120_P	1.996	1.00
36_I	180_I	1.959	1.00
41_R	45_G	1.918	1.00
38_I	44_P	1.906	1.00
77_I	100_V	1.872	1.00
84_A	95_V	1.871	1.00
78_A	92_P	1.847	1.00
176_M	180_I	1.814	1.00
84_A	90_I	1.806	1.00
77_I	97_V	1.772	1.00
36_I	184_L	1.725	1.00
53_I	133_S	1.722	1.00
76_A	115_V	1.684	1.00
112_V	176_M	1.663	1.00
50_Q	53_I	1.645	1.00
46_L	181_I	1.619	1.00
182_R	186_L	1.585	1.00
70_D	128_S	1.563	1.00
76_A	79_A	1.548	1.00
97_V	117_G	1.546	1.00
37_P	119_I	1.504	1.00
62_V	171_Y	1.504	1.00
165_L	172_F	1.495	1.00
102_P	183_E	1.488	1.00
41_R	137_E	1.482	1.00
68_A	110_Y	1.450	1.00
173_V	181_I	1.449	1.00
73_D	78_A	1.449	1.00
50_Q	133_S	1.441	1.00
31_Q	69_V	1.429	1.00
47_L	88_V	1.416	1.00
62_V	136_F	1.399	1.00
50_Q	134_A	1.399	1.00
48_L	177_T	1.383	1.00
50_Q	171_Y	1.350	1.00
91_P	94_A	1.348	1.00
58_H	61_Q	1.325	1.00
89_A	127_A	1.314	1.00
168_Y	173_V	1.310	1.00
54_H	130_D	1.281	1.00
100_V	115_V	1.279	1.00
106_S	176_M	1.271	1.00
151_P	162_R	1.254	1.00
49_T	55_L	1.247	1.00
144_L	185_A	1.245	1.00
39_V	137_E	1.240	1.00
136_F	171_Y	1.216	1.00
155_Y	160_S	1.203	1.00
81_L	85_E	1.203	1.00
153_D	160_S	1.187	1.00
143_A	185_A	1.184	1.00
112_V	180_I	1.170	1.00
40_R	44_P	1.161	1.00
55_L	59_A	1.142	1.00
30_R	68_A	1.141	1.00
85_E	91_P	1.134	1.00
139_P	142_Q	1.129	1.00
37_P	117_G	1.102	1.00
103_P	113_T	1.079	1.00
103_P	111_Q	1.078	1.00
31_Q	111_Q	1.059	1.00
104_V	179_G	1.053	1.00
116_V	184_L	1.051	1.00
149_Y	182_R	1.030	0.99
52_S	55_L	1.023	0.99
62_V	173_V	1.022	0.99
49_T	132_V	1.012	0.99
64_F	180_I	1.004	0.99
108_T	176_M	0.988	0.99
40_R	118_I	0.978	0.99
167_W	170_Q	0.974	0.99
49_T	58_H	0.952	0.99
84_A	115_V	0.951	0.99
32_A	110_Y	0.948	0.99
39_V	45_G	0.946	0.99
34_V	180_I	0.936	0.99
145_H	148_R	0.931	0.99
125_Y	135_V	0.931	0.99
36_I	46_L	0.929	0.99
72_T	78_A	0.924	0.99
73_D	79_A	0.915	0.99
55_L	58_H	0.914	0.99
143_A	181_I	0.913	0.99
138_M	173_V	0.912	0.99
164_W	182_R	0.905	0.99
48_L	62_V	0.897	0.99
92_P	95_V	0.892	0.98
47_L	119_I	0.888	0.98
76_A	113_T	0.885	0.98
53_I	59_A	0.882	0.98
48_L	64_F	0.877	0.98
81_L	97_V	0.872	0.98
149_Y	166_S	0.871	0.98
142_Q	168_Y	0.870	0.98
61_Q	110_Y	0.864	0.98
101_L	116_V	0.860	0.98
30_R	110_Y	0.859	0.98
94_A	123_L	0.859	0.98
156_R	159_D	0.852	0.98
33_A	76_A	0.836	0.98
52_S	59_A	0.825	0.98
153_D	162_R	0.819	0.97
44_P	118_I	0.811	0.97
149_Y	185_A	0.805	0.97
106_S	110_Y	0.798	0.97
142_Q	148_R	0.798	0.97
29_H	105_D	0.794	0.97
94_A	120_P	0.794	0.97
35_L	97_V	0.792	0.97
26_T	29_H	0.788	0.97
49_T	57_K	0.785	0.97
85_E	93_S	0.781	0.97
84_A	88_V	0.778	0.96
140_L	144_L	0.777	0.96
120_P	123_L	0.777	0.96
48_L	185_A	0.771	0.96
155_Y	159_D	0.770	0.96
110_Y	176_M	0.768	0.96
141_A	145_H	0.767	0.96
31_Q	103_P	0.758	0.96
53_I	60_G	0.756	0.96
105_D	111_Q	0.754	0.96
81_L	95_V	0.749	0.96
36_I	64_F	0.749	0.96
85_E	126_R	0.747	0.96
142_Q	169_E	0.747	0.96
155_Y	158_G	0.746	0.95
97_V	115_V	0.743	0.95
96_E	118_I	0.734	0.95
35_L	80_A	0.731	0.95
56_R	59_A	0.725	0.95
152_L	165_L	0.725	0.95
167_W	172_F	0.722	0.95
61_Q	107_V	0.722	0.95
142_Q	173_V	0.719	0.95
168_Y	171_Y	0.716	0.94
75_S	79_A	0.712	0.94
101_L	114_P	0.712	0.94
35_L	95_V	0.708	0.94
38_I	140_L	0.707	0.94
33_A	114_P	0.699	0.94
37_P	64_F	0.696	0.94
150_H	167_W	0.688	0.93
57_K	108_T	0.677	0.93
57_K	110_Y	0.676	0.93
98_I	118_I	0.673	0.92
153_D	156_R	0.672	0.92
37_P	65_P	0.668	0.92
88_V	127_A	0.668	0.92
144_L	188_I	0.667	0.92
49_T	88_V	0.666	0.92
88_V	132_V	0.663	0.92
179_G	183_E	0.658	0.91
48_L	136_F	0.648	0.91
88_V	135_V	0.648	0.91
100_V	113_T	0.642	0.90
164_W	179_G	0.637	0.90
148_R	166_S	0.635	0.90
77_I	81_L	0.631	0.90
88_V	125_Y	0.629	0.90
38_I	116_V	0.621	0.89
22_I	25_E	0.621	0.89
46_L	140_L	0.619	0.89
47_L	64_F	0.617	0.89
143_A	166_S	0.616	0.89
156_R	162_R	0.613	0.88
51_R	132_V	0.609	0.88
63_A	84_A	0.607	0.88
166_S	185_A	0.606	0.88
80_A	84_A	0.605	0.88
173_V	178_A	0.604	0.88
31_Q	76_A	0.601	0.87
83_E	131_E	0.600	0.87
62_V	168_Y	0.599	0.87
154_I	165_L	0.598	0.87
55_L	130_D	0.595	0.87
64_F	104_V	0.595	0.87
139_P	168_Y	0.593	0.87
81_L	117_G	0.590	0.86
89_A	128_S	0.590	0.86
95_V	119_I	0.590	0.86
61_Q	108_T	0.589	0.86
55_L	63_A	0.589	0.86
92_P	117_G	0.588	0.86
38_I	45_G	0.586	0.86
94_A	121_P	0.576	0.85
81_L	92_P	0.576	0.85
106_S	109_G	0.575	0.85
46_L	143_A	0.572	0.85
38_I	184_L	0.570	0.84
64_F	185_A	0.561	0.84
64_F	181_I	0.560	0.83
149_Y	164_W	0.560	0.83
93_S	124_P	0.559	0.83
41_R	122_D	0.557	0.83
176_M	183_E	0.556	0.83
100_V	103_P	0.556	0.83
104_V	183_E	0.553	0.83
37_P	48_L	0.553	0.83
24_R	28_N	0.550	0.82
114_P	180_I	0.550	0.82
38_I	46_L	0.546	0.82
107_V	110_Y	0.546	0.82
84_A	89_A	0.540	0.81
183_E	187_Q	0.539	0.81
49_T	52_S	0.536	0.81
58_H	178_A	0.533	0.80
37_P	40_R	0.533	0.80
124_P	127_A	0.530	0.80
46_L	185_A	0.528	0.80
37_P	47_L	0.528	0.80
43_Q	139_P	0.527	0.80
22_I	27_L	0.526	0.79
148_R	153_D	0.524	0.79
146_L	149_Y	0.523	0.79
49_T	61_Q	0.519	0.79
127_A	132_V	0.519	0.79
62_V	174_W	0.519	0.79
57_K	107_V	0.518	0.78
102_P	114_P	0.515	0.78
133_S	171_Y	0.515	0.78
106_S	179_G	0.515	0.78
55_L	178_A	0.514	0.78
109_G	176_M	0.513	0.78
58_H	108_T	0.509	0.77
29_H	111_Q	0.508	0.77
43_Q	159_D	0.508	0.77
166_S	182_R	0.507	0.77
97_V	118_I	0.505	0.77
35_L	64_F	0.505	0.77
127_A	130_D	0.505	0.77
32_A	134_A	0.505	0.77
138_M	168_Y	0.505	0.77
154_I	157_R	0.503	0.76
68_A	136_F	0.500	0.76

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
1nqzA	1	0.849	100	0.515	Contact Map
3h95A	2	0.7708	99.8	0.635	Contact Map
4c9xA	2	0.7708	99.8	0.669	Contact Map
4nfwA	6	0.7604	99.7	0.68	Contact Map
5bonA	4	0.7812	99.7	0.681	Contact Map
3kvhA	2	0.7812	99.7	0.686	Contact Map
2w4eA	2	0.7031	99.7	0.688	Contact Map
3qsjA	1	0.776	99.7	0.691	Contact Map
3fjyA	2	0.7708	99.7	0.697	Contact Map
1u20A	2	0.849	99.7	0.698	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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