NUDG - ECOLI - GREMLIN Contacts

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NUDG - CTP pyrophosphohydrolase

UniProt:	P77788	Sequences: MKMIEVVAAIIERDGKILLAQRPAQSDQAGLWEFAGGKVEPDESQRQALVRELREELGIEATVGEYVASHQREVSGRIIHLHAWHVPDFHGTLQAHEHQALVWCSPEEALQYPLAPADIPLLEAFMALRAARPAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14009
Length:	135 (120)
Sequences:	5931 (4306)
Seq/√Len:	393.1

ECOLI - NUDG MUTT NUDJ YFCD NUDC NUDI
BACSU - YVCI MUTT YJHB
HALSA - Q9HR46 Q9HS29 IDI
SULSO - Q97WE7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_E	16_K	3.697	1.00
54_R	60_E	3.675	1.00
21_Q	100_A	2.971	1.00
44_S	47_Q	2.948	1.00
39_V	48_A	2.871	1.00
21_Q	99_Q	2.552	1.00
105_S	108_E	2.348	1.00
19_L	112_Y	2.234	1.00
53_L	61_A	2.120	1.00
19_L	104_C	2.094	1.00
104_C	112_Y	2.040	1.00
16_K	105_S	2.036	1.00
18_L	101_L	2.008	1.00
31_L	113_P	2.002	1.00
62_T	87_P	1.943	1.00
19_L	114_L	1.850	1.00
5_E	80_H	1.812	1.00
25_Q	29_A	1.811	1.00
50_V	54_R	1.762	1.00
68_A	124_A	1.756	1.00
59_I	88_D	1.655	1.00
64_G	87_P	1.627	1.00
60_E	90_H	1.599	1.00
45_Q	84_W	1.558	1.00
71_Q	78_I	1.509	1.00
5_E	82_H	1.492	1.00
108_E	111_Q	1.485	1.00
58_G	96_H	1.447	1.00
66_Y	82_H	1.432	1.00
66_Y	69_S	1.426	1.00
39_V	45_Q	1.400	1.00
88_D	91_G	1.370	1.00
20_A	98_H	1.368	1.00
20_A	101_L	1.346	1.00
15_G	106_P	1.289	1.00
58_G	94_Q	1.279	1.00
69_S	80_H	1.267	1.00
62_T	89_F	1.265	1.00
50_V	63_V	1.265	1.00
23_P	29_A	1.259	1.00
8_A	83_A	1.228	1.00
95_A	98_H	1.222	1.00
102_V	112_Y	1.207	1.00
7_V	48_A	1.198	1.00
73_E	78_I	1.197	1.00
61_A	86_V	1.155	1.00
21_Q	30_G	1.154	1.00
93_L	101_L	1.136	1.00
8_A	49_L	1.126	1.00
69_S	82_H	1.119	1.00
28_Q	31_L	1.117	1.00
9_A	49_L	1.109	1.00
30_G	99_Q	1.082	1.00
71_Q	80_H	1.082	1.00
59_I	93_L	1.068	1.00
54_R	58_G	1.043	1.00
9_A	53_L	1.027	1.00
46_R	50_V	1.012	1.00
120_P	123_E	1.011	1.00
23_P	99_Q	1.003	1.00
65_E	85_H	1.002	1.00
73_E	76_G	0.997	1.00
11_I	53_L	0.997	1.00
24_A	29_A	0.987	1.00
67_V	85_H	0.982	1.00
52_E	56_E	0.979	1.00
7_V	45_Q	0.965	1.00
49_L	86_V	0.956	1.00
12_E	15_G	0.952	1.00
66_Y	84_W	0.937	1.00
119_I	123_E	0.931	1.00
114_L	118_D	0.928	1.00
47_Q	50_V	0.920	1.00
95_A	101_L	0.916	1.00
45_Q	82_H	0.905	1.00
31_L	115_A	0.905	1.00
115_A	118_D	0.898	1.00
31_L	116_P	0.893	1.00
63_V	86_V	0.874	1.00
102_V	108_E	0.872	1.00
50_V	61_A	0.851	1.00
110_L	123_E	0.846	1.00
53_L	86_V	0.841	1.00
49_L	84_W	0.816	1.00
10_I	67_V	0.815	1.00
24_A	99_Q	0.811	1.00
62_T	88_D	0.806	1.00
18_L	59_I	0.805	1.00
22_R	33_E	0.804	1.00
86_V	89_F	0.802	1.00
68_A	71_Q	0.800	1.00
21_Q	32_W	0.795	1.00
83_A	121_L	0.787	1.00
27_D	77_R	0.786	1.00
13_R	16_K	0.785	1.00
61_A	64_G	0.779	1.00
24_A	30_G	0.774	1.00
72_R	75_S	0.773	1.00
32_W	102_V	0.773	1.00
74_V	77_R	0.772	1.00
77_R	81_L	0.769	1.00
50_V	60_E	0.753	1.00
49_L	53_L	0.750	1.00
33_E	98_H	0.730	1.00
50_V	64_G	0.725	1.00
12_E	85_H	0.722	1.00
16_K	108_E	0.720	1.00
5_E	9_A	0.720	1.00
23_P	97_E	0.718	1.00
22_R	98_H	0.706	1.00
12_E	17_I	0.700	1.00
72_R	79_I	0.688	0.99
50_V	62_T	0.680	0.99
64_G	85_H	0.672	0.99
63_V	87_P	0.670	0.99
85_H	125_F	0.670	0.99
28_Q	115_A	0.669	0.99
22_R	38_K	0.663	0.99
63_V	88_D	0.660	0.99
60_E	89_F	0.644	0.99
90_H	93_L	0.642	0.99
34_F	118_D	0.640	0.99
10_I	83_A	0.638	0.99
53_L	59_I	0.637	0.99
68_A	121_L	0.637	0.99
34_F	83_A	0.635	0.99
95_A	99_Q	0.632	0.99
9_A	86_V	0.630	0.99
9_A	12_E	0.626	0.99
52_E	55_E	0.625	0.99
57_L	101_L	0.622	0.99
7_V	11_I	0.620	0.99
72_R	77_R	0.603	0.99
32_W	104_C	0.603	0.99
33_E	79_I	0.597	0.99
22_R	25_Q	0.596	0.99
32_W	100_A	0.595	0.99
105_S	109_A	0.593	0.98
7_V	10_I	0.587	0.98
27_D	76_G	0.585	0.98
6_V	118_D	0.582	0.98
46_R	84_W	0.582	0.98
95_A	100_A	0.581	0.98
43_E	48_A	0.580	0.98
29_A	99_Q	0.578	0.98
35_A	57_L	0.572	0.98
104_C	110_L	0.566	0.98
110_L	119_I	0.565	0.98
63_V	89_F	0.563	0.98
118_D	121_L	0.560	0.98
59_I	91_G	0.556	0.98
63_V	84_W	0.553	0.98
13_R	87_P	0.552	0.98
20_A	49_L	0.552	0.98
9_A	61_A	0.552	0.98
6_V	22_R	0.551	0.98
13_R	91_G	0.550	0.98
13_R	92_T	0.549	0.98
114_L	122_L	0.549	0.98
79_I	82_H	0.547	0.97
21_Q	31_L	0.537	0.97
19_L	32_W	0.535	0.97
67_V	124_A	0.535	0.97
63_V	66_Y	0.532	0.97
49_L	63_V	0.531	0.97
17_I	34_F	0.530	0.97
15_G	105_S	0.525	0.97
23_P	30_G	0.525	0.97
33_E	118_D	0.524	0.97
20_A	57_L	0.523	0.97
54_R	96_H	0.522	0.97
54_R	57_L	0.521	0.97
70_H	81_L	0.516	0.96
33_E	115_A	0.513	0.96
78_I	81_L	0.512	0.96
33_E	36_G	0.505	0.96
20_A	38_K	0.505	0.96
20_A	103_W	0.504	0.96
38_K	79_I	0.504	0.96
64_G	86_V	0.500	0.96

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
2rrkA	1	1	99.9	0.266	Contact Map
3gwyA	2	0.963	99.9	0.288	Contact Map
1mutA	1	0.9481	99.9	0.292	Contact Map
3eesA	2	0.9704	99.9	0.314	Contact Map
3hhjA	1	0.9333	99.9	0.321	Contact Map
4v14A	1	0.9185	99.9	0.329	Contact Map
3fk9A	2	0.9556	99.9	0.33	Contact Map
3grnA	2	0.963	99.9	0.331	Contact Map
3r03A	2	0.9407	99.9	0.331	Contact Map
3i7uA	4	0.9556	99.9	0.332	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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