GCSH - HALSA - GREMLIN Contacts

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GCSH - Probable glycine cleavage system H protein

UniProt:	Q9HPJ8	Sequences: MSFDVPDDLQYLESHEWIDPATGRVGISEFAQDELGDVVFVELPSVGDALDQHDELGVVESIKAVSDLYAPVSGEVTAVNDALTNEPELVNEAPFGDGWLVEIDFDSDDLEATLDSDDYRAQIA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	124 (119)
Sequences:	3709 (2307)
Seq/√Len:	211.5

ECOLI - GCSH
BACSU - GCSH
HALSA - GCSH
SULSO - GCSH1 GCSH2 GCSH3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_D	118_D	4.191	1.00
93_A	96_G	3.521	1.00
75_E	104_D	3.494	1.00
56_L	101_V	3.173	1.00
24_R	102_E	3.073	1.00
78_A	102_E	2.778	1.00
29_E	32_Q	2.216	1.00
23_G	105_F	2.171	1.00
93_A	97_D	2.065	1.00
73_S	109_D	2.028	1.00
22_T	102_E	2.010	1.00
21_A	104_D	1.986	1.00
114_L	122_Q	1.935	1.00
49_A	75_E	1.905	1.00
50_L	70_A	1.839	1.00
116_S	120_R	1.819	1.00
108_D	111_E	1.779	1.00
106_D	109_D	1.766	1.00
86_E	89_L	1.757	1.00
9_L	95_F	1.727	1.00
90_V	100_L	1.569	1.00
72_V	105_F	1.569	1.00
29_E	33_D	1.541	1.00
58_V	65_V	1.499	1.00
82_A	86_E	1.493	1.00
57_G	68_L	1.492	1.00
51_D	54_D	1.474	1.00
45_S	48_D	1.457	1.00
52_Q	112_A	1.455	1.00
51_D	73_S	1.399	1.00
55_E	67_D	1.388	1.00
82_A	97_D	1.378	1.00
13_E	122_Q	1.370	1.00
22_T	104_D	1.361	1.00
47_G	75_E	1.354	1.00
83_L	100_L	1.319	1.00
89_L	98_G	1.314	1.00
32_Q	91_N	1.289	1.00
18_I	23_G	1.287	1.00
56_L	68_L	1.254	1.00
43_L	79_V	1.253	1.00
58_V	62_I	1.219	1.00
30_F	34_E	1.198	1.00
82_A	89_L	1.187	1.00
50_L	56_L	1.176	1.00
25_V	101_V	1.138	1.00
81_D	84_T	1.137	1.00
10_Q	110_L	1.134	1.00
16_E	62_I	1.131	1.00
86_E	92_E	1.110	1.00
42_E	58_V	1.107	1.00
7_D	117_D	1.107	1.00
52_Q	109_D	1.085	1.00
39_V	62_I	1.082	1.00
22_T	77_T	1.071	1.00
118_D	121_A	1.061	1.00
77_T	104_D	1.057	1.00
117_D	120_R	1.055	1.00
74_G	103_I	1.043	1.00
41_V	83_L	0.998	1.00
43_L	100_L	0.980	1.00
18_I	72_V	0.962	1.00
48_D	54_D	0.961	1.00
23_G	72_V	0.961	1.00
12_L	18_I	0.950	1.00
10_Q	111_E	0.948	1.00
5_V	120_R	0.943	0.99
46_V	79_V	0.938	0.99
72_V	103_I	0.921	0.99
78_A	81_D	0.910	0.99
12_L	16_E	0.900	0.99
89_L	92_E	0.896	0.99
7_D	120_R	0.892	0.99
41_V	59_V	0.884	0.99
27_I	59_V	0.872	0.99
89_L	97_D	0.869	0.99
14_S	69_Y	0.849	0.99
58_V	67_D	0.845	0.99
68_L	101_V	0.844	0.99
95_F	116_S	0.836	0.99
17_W	26_G	0.836	0.99
82_A	85_N	0.833	0.99
5_V	116_S	0.828	0.99
12_L	28_S	0.822	0.99
107_S	110_L	0.807	0.98
14_S	64_A	0.807	0.98
70_A	103_I	0.800	0.98
39_V	65_V	0.790	0.98
106_D	110_L	0.786	0.98
46_V	78_A	0.785	0.98
88_E	92_E	0.768	0.98
37_D	88_E	0.765	0.98
35_L	66_S	0.760	0.98
81_D	85_N	0.760	0.98
11_Y	95_F	0.756	0.98
10_Q	115_D	0.755	0.98
6_P	116_S	0.750	0.97
25_V	103_I	0.750	0.97
15_H	36_G	0.749	0.97
29_E	95_F	0.747	0.97
23_G	110_L	0.746	0.97
83_L	89_L	0.746	0.97
32_Q	95_F	0.744	0.97
5_V	95_F	0.723	0.97
38_V	59_V	0.719	0.97
22_T	78_A	0.709	0.96
107_S	111_E	0.695	0.96
5_V	123_I	0.690	0.96
34_E	61_S	0.689	0.96
68_L	100_L	0.668	0.95
50_L	76_V	0.667	0.95
21_A	105_F	0.664	0.95
50_L	73_S	0.664	0.95
44_P	76_V	0.658	0.95
63_K	66_S	0.656	0.94
114_L	118_D	0.654	0.94
31_A	66_S	0.653	0.94
19_D	22_T	0.652	0.94
44_P	79_V	0.642	0.94
45_S	85_N	0.639	0.94
6_P	28_S	0.635	0.93
35_L	64_A	0.634	0.93
13_E	118_D	0.628	0.93
16_E	39_V	0.624	0.93
44_P	61_S	0.618	0.93
92_E	97_D	0.618	0.93
23_G	109_D	0.613	0.92
46_V	81_D	0.611	0.92
13_E	112_A	0.611	0.92
14_S	53_H	0.608	0.92
8_D	116_S	0.606	0.92
39_V	60_E	0.602	0.92
28_S	94_P	0.601	0.91
11_Y	28_S	0.599	0.91
29_E	91_N	0.596	0.91
106_D	111_E	0.595	0.91
38_V	57_G	0.595	0.91
41_V	87_P	0.592	0.91
61_S	64_A	0.590	0.91
93_A	98_G	0.588	0.91
12_L	113_T	0.586	0.90
70_A	76_V	0.584	0.90
117_D	121_A	0.584	0.90
16_E	69_Y	0.583	0.90
60_E	63_K	0.580	0.90
25_V	71_P	0.579	0.90
34_E	66_S	0.565	0.89
47_G	77_T	0.564	0.89
48_D	51_D	0.561	0.88
105_F	110_L	0.558	0.88
21_A	24_R	0.556	0.88
76_V	101_V	0.553	0.88
38_V	58_V	0.551	0.88
22_T	105_F	0.550	0.87
6_P	11_Y	0.547	0.87
5_V	29_E	0.545	0.87
16_E	31_A	0.544	0.87
16_E	64_A	0.543	0.87
32_Q	64_A	0.541	0.87
38_V	91_N	0.539	0.86
27_I	31_A	0.538	0.86
61_S	65_V	0.537	0.86
19_D	23_G	0.533	0.86
36_G	66_S	0.532	0.86
46_V	75_E	0.531	0.86
40_F	60_E	0.522	0.85
55_E	64_A	0.517	0.84
37_D	62_I	0.514	0.84
11_Y	116_S	0.514	0.84
9_L	116_S	0.512	0.84
55_E	84_T	0.512	0.84
57_G	101_V	0.508	0.83
10_Q	37_D	0.508	0.83
40_F	63_K	0.507	0.83
38_V	56_L	0.502	0.82
31_A	63_K	0.501	0.82
48_D	85_N	0.501	0.82
19_D	102_E	0.500	0.82

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
3hgbA	1	0.9919	100	0.163	Contact Map
3tzuA	2	0.9516	100	0.216	Contact Map
3mxuA	3	0.9919	100	0.223	Contact Map
1hpcA	2	0.9839	100	0.259	Contact Map
3a7lA	1	0.9839	100	0.265	Contact Map
3wdnA	1	0.9516	100	0.29	Contact Map
1onlA	1	0.9758	100	0.305	Contact Map
1zkoA	2	1	100	0.321	Contact Map
5a35A	1	0.879	100	0.361	Contact Map
1gjxA	1	0.6532	96.3	0.854	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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