TAGD - BACSU - GREMLIN Contacts

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TAGD - Glycerol-3-phosphate cytidylyltransferase

UniProt:	P27623	Sequences: MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEIAGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	129 (123)
Sequences:	2936 (1802)
Seq/√Len:	162.5

ECOLI - HLDE
BACSU - TAGD
HALSA - RIBL
SULSO - Q97ZG4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_V	28_G	3.609	1.00
52_Y	70_P	2.934	1.00
9_T	41_N	2.337	1.00
43_Q	74_W	2.312	1.00
25_K	66_D	2.267	1.00
54_H	117_I	2.237	1.00
30_Y	67_E	2.163	1.00
5_I	34_A	2.082	1.00
79_Q	82_I	2.017	1.00
101_F	105_Q	2.009	1.00
19_K	57_L	1.944	1.00
22_E	64_Y	1.933	1.00
99_F	103_K	1.926	1.00
35_I	56_K	1.854	1.00
3_K	30_Y	1.841	1.00
19_K	22_E	1.780	1.00
51_S	54_H	1.736	1.00
56_K	60_E	1.703	1.00
56_K	68_V	1.688	1.00
100_D	104_D	1.682	1.00
13_L	62_I	1.679	1.00
37_T	70_P	1.675	1.00
23_R	26_Q	1.669	1.00
52_Y	56_K	1.656	1.00
102_L	105_Q	1.611	1.00
57_L	60_E	1.588	1.00
22_E	57_L	1.582	1.00
24_A	90_V	1.556	1.00
37_T	72_K	1.501	1.00
56_K	70_P	1.492	1.00
18_I	58_I	1.468	1.00
93_D	112_P	1.467	1.00
39_E	43_Q	1.432	1.00
15_W	54_H	1.417	1.00
12_L	50_H	1.406	1.00
19_K	23_R	1.401	1.00
119_T	123_K	1.399	1.00
78_K	82_I	1.396	1.00
42_L	47_K	1.371	1.00
73_N	79_Q	1.335	1.00
15_W	117_I	1.327	1.00
25_K	30_Y	1.291	1.00
50_H	54_H	1.288	1.00
19_K	114_T	1.285	1.00
13_L	18_I	1.258	1.00
13_L	58_I	1.241	1.00
99_F	102_L	1.232	1.00
15_W	58_I	1.226	1.00
4_V	90_V	1.214	1.00
24_A	31_L	1.202	1.00
95_W	98_K	1.200	1.00
95_W	105_Q	1.189	1.00
78_K	105_Q	1.184	1.00
39_E	72_K	1.147	1.00
49_Y	123_K	1.144	1.00
121_K	124_E	1.135	1.00
78_K	101_F	1.134	1.00
10_F	20_L	1.112	1.00
85_N	104_D	1.083	0.99
93_D	110_Y	1.071	0.99
102_L	106_C	1.042	0.99
23_R	111_L	1.026	0.99
97_G	103_K	1.023	0.99
81_I	89_F	1.012	0.99
98_K	102_L	1.003	0.99
13_L	59_L	1.000	0.99
27_L	109_V	0.995	0.99
36_S	40_F	0.990	0.99
121_K	125_E	0.982	0.99
82_I	104_D	0.971	0.99
22_E	26_Q	0.963	0.99
35_I	59_L	0.960	0.99
20_L	113_R	0.943	0.99
114_T	117_I	0.943	0.99
21_L	64_Y	0.928	0.98
27_L	88_V	0.926	0.98
23_R	112_P	0.919	0.98
27_L	90_V	0.919	0.98
97_G	102_L	0.904	0.98
96_E	100_D	0.899	0.98
28_G	90_V	0.893	0.98
41_N	44_K	0.884	0.98
97_G	101_F	0.879	0.98
34_A	69_I	0.877	0.98
78_K	104_D	0.876	0.98
3_K	67_E	0.867	0.98
42_L	46_K	0.867	0.98
37_T	52_Y	0.852	0.97
76_Q	89_F	0.844	0.97
21_L	24_A	0.842	0.97
15_W	19_K	0.833	0.97
99_F	105_Q	0.829	0.97
25_K	63_R	0.820	0.97
33_V	59_L	0.811	0.96
50_H	122_I	0.806	0.96
95_W	110_Y	0.798	0.96
97_G	105_Q	0.797	0.96
50_H	58_I	0.787	0.96
101_F	104_D	0.782	0.96
89_F	97_G	0.772	0.95
98_K	105_Q	0.771	0.95
15_W	18_I	0.759	0.95
60_E	67_E	0.758	0.95
27_L	111_L	0.757	0.95
4_V	27_L	0.756	0.95
61_T	64_Y	0.748	0.94
6_T	10_F	0.739	0.94
6_T	20_L	0.734	0.94
40_F	71_E	0.729	0.94
18_I	62_I	0.729	0.94
36_S	71_E	0.718	0.93
112_P	115_E	0.717	0.93
95_W	102_L	0.697	0.92
15_W	50_H	0.696	0.92
95_W	100_D	0.688	0.91
98_K	101_F	0.688	0.91
7_Y	89_F	0.688	0.91
97_G	100_D	0.685	0.91
7_Y	34_A	0.681	0.91
18_I	61_T	0.680	0.91
34_A	80_D	0.679	0.91
95_W	99_F	0.676	0.91
65_V	68_V	0.674	0.91
90_V	111_L	0.666	0.90
88_V	107_E	0.662	0.90
53_E	70_P	0.655	0.89
79_Q	83_D	0.654	0.89
7_Y	91_M	0.653	0.89
7_Y	71_E	0.652	0.89
18_I	64_Y	0.651	0.89
3_K	86_I	0.648	0.89
36_S	44_K	0.630	0.87
57_L	61_T	0.630	0.87
82_I	107_E	0.628	0.87
98_K	106_C	0.621	0.87
22_E	61_T	0.618	0.86
15_W	57_L	0.615	0.86
116_G	121_K	0.614	0.86
97_G	104_D	0.613	0.86
6_T	21_L	0.611	0.86
59_L	68_V	0.611	0.86
22_E	63_R	0.606	0.85
117_I	121_K	0.599	0.85
42_L	48_A	0.599	0.85
67_E	70_P	0.598	0.85
15_W	114_T	0.596	0.84
85_N	105_Q	0.596	0.84
41_N	46_K	0.595	0.84
93_D	111_L	0.594	0.84
33_V	65_V	0.591	0.84
5_I	89_F	0.586	0.83
82_I	100_D	0.585	0.83
88_V	109_V	0.581	0.83
37_T	71_E	0.580	0.83
35_I	68_V	0.579	0.83
82_I	85_N	0.575	0.82
123_K	126_I	0.574	0.82
3_K	87_D	0.573	0.82
58_I	62_I	0.570	0.82
23_R	114_T	0.568	0.81
8_G	11_D	0.563	0.81
32_V	86_I	0.562	0.81
81_I	86_I	0.560	0.81
28_G	88_V	0.551	0.80
71_E	91_M	0.551	0.80
78_K	81_I	0.546	0.79
4_V	88_V	0.546	0.79
109_V	112_P	0.544	0.79
32_V	84_H	0.544	0.79
44_K	74_W	0.542	0.78
93_D	113_R	0.541	0.78
5_I	81_I	0.536	0.78
49_Y	121_K	0.535	0.78
22_E	60_E	0.534	0.77
81_I	106_C	0.530	0.77
96_E	99_F	0.523	0.76
3_K	84_H	0.523	0.76
89_F	110_Y	0.516	0.75
41_N	45_Q	0.516	0.75
19_K	110_Y	0.515	0.75
54_H	58_I	0.505	0.73
36_S	47_K	0.504	0.73
78_K	100_D	0.502	0.73
19_K	115_E	0.500	0.73

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
3elbA	2	0.9922	100	0.33	Contact Map
4mvcA	2	1	100	0.4	Contact Map
3hl4A	2	1	99.9	0.427	Contact Map
1cozA	2	0.9767	99.9	0.466	Contact Map
2b7lA	2	0.8915	99.9	0.482	Contact Map
3glvA	2	0.8682	99.8	0.532	Contact Map
3k9wA	5	0.9612	99.7	0.616	Contact Map
3do8A	2	0.8915	99.6	0.625	Contact Map
3nbkA	5	0.9612	99.6	0.637	Contact Map
3op1A	4	0.9922	99.6	0.639	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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