OPENSEQ.org - DHSC - ECOLI GREMLIN

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DHSC - Succinate dehydrogenase cytochrome b556 subunit

UniProt:	P69054	Sequence MIRNVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQASAIMGSFFVKFIMWGILTALAYHVVVGIRHMMMDFGYLEETFEAGKRSAKISFVITVVLSLLAGVLVW	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10933
Length:	129 (128)
Sequences:	734
Seq/Len:	5.73

DHSC
Paralog alert: 0.05 [within 20: 0.01] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
86_V	116_I	3.711	1.00
20_F	24_A	3.312	1.00
21_P	24_A	2.599	1.00
86_V	120_L	2.385	1.00
14_D	17_T	2.243	1.00
20_F	25_I	2.19	1.00
96_F	99_L	2.18	1.00
102_T	105_A	2.14	1.00
90_R	109_S	2.006	1.00
103_F	107_K	1.904	1.00
89_I	93_M	1.883	1.00
84_H	88_G	1.878	1.00
118_V	122_L	1.857	1.00
55_P	59_E	1.801	1.00
34_G	88_G	1.6	0.99
92_M	96_F	1.592	0.99
34_G	84_H	1.587	0.99
13_L	18_I	1.552	0.99
104_E	108_R	1.473	0.99
22_I	107_K	1.471	0.99
107_K	111_K	1.465	0.99
12_N	17_T	1.428	0.98
26_A	83_Y	1.41	0.98
13_L	17_T	1.392	0.98
12_N	18_I	1.388	0.98
82_A	124_A	1.356	0.97
87_V	113_S	1.33	0.97
111_K	115_V	1.32	0.97
105_A	109_S	1.316	0.97
120_L	124_A	1.26	0.96
26_A	114_F	1.254	0.95
93_M	96_F	1.24	0.95
79_T	121_S	1.206	0.94
51_S	54_S	1.182	0.93
79_T	117_T	1.176	0.93
78_L	125_G	1.171	0.93
94_M	106_G	1.169	0.93
86_V	113_S	1.167	0.93
73_I	76_G	1.135	0.91
39_V	77_I	1.119	0.90
17_T	33_S	1.113	0.90
26_A	94_M	1.111	0.90
79_T	83_Y	1.109	0.90
82_A	120_L	1.083	0.88
110_A	113_S	1.054	0.87
13_L	129_W	1.044	0.86
119_V	123_L	1.044	0.86
44_L	77_I	1.041	0.86
32_V	35_V	1.026	0.85
33_S	49_G	1.018	0.84
25_I	29_L	1.016	0.84
17_T	20_F	1.015	0.84
76_G	79_T	1.015	0.84
116_I	120_L	1.011	0.83
108_R	111_K	1.007	0.83
42_G	51_S	1.007	0.83
32_V	65_M	1.002	0.83

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
3vr8C	2	0.969	100	0.19	Contact Map	0.626
2wdqC	3	0.9922	100	0.195	Contact Map	0.615
1zoyC	1	0.9535	100	0.206	Contact Map	0.61
2h88C	2	0.9535	100	0.213	Contact Map	0.631
2wdqD	3	0.8682	99.5	0.626	Contact Map	0.283
2bs2C	2	0.9535	95	0.851	Contact Map	0.326
1kf6C	2	0.907	66.2	0.901	Contact Map	0.264
1kf6D	2	0.8605	64.2	0.903	Contact Map	0.578
2h88D	2	0.6667	16.8	0.93	Contact Map	0.332
2nr9A	1	0.7752	2.9	0.951	Contact Map	0.19

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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