OPENSEQ.org - YCIF - ECOLI GREMLIN

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YCIF - Protein YciF

UniProt:	P21362	Sequence MNMKTIEDVFIHLLSDTYSAEKQLTRALAKLARATSNEKLSQAFHAHLEETHGQIERIDQVVESESNLKIKRMKCVAMEGLIEEANEVIESTEKNEVRDAALIAAAQKVEHYEIASYGTLATLAEQLGYRKAAKLLKETLEEEKATDIKLTDLAINNVNKKAENKA	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11126
Length:	166 (162)
Sequences:	321
Seq/Len:	1.98

YCIF
Paralog alert: 0.22 [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
44_F	102_L	2.912	1.00
50_E	145_A	2.593	1.00
108_K	116_S	2.326	1.00
137_K	141_E	2.252	1.00
12_H	73_M	2.22	1.00
121_A	137_K	2.172	1.00
44_F	106_A	1.982	0.99
57_R	142_E	1.961	0.99
57_R	139_T	1.76	0.97
17_T	120_L	1.701	0.96
16_D	75_C	1.644	0.95
46_A	149_K	1.595	0.94
41_S	45_H	1.592	0.94
19_S	79_E	1.573	0.93
25_T	52_H	1.54	0.92
24_L	78_M	1.534	0.92
19_S	78_M	1.515	0.91
38_E	41_S	1.51	0.91
46_A	146_T	1.487	0.90
13_L	108_K	1.472	0.90
125_E	133_A	1.463	0.89
7_E	129_Y	1.445	0.89
107_Q	118_G	1.439	0.88
25_T	55_I	1.407	0.87
16_D	112_Y	1.366	0.85
34_A	89_I	1.344	0.83
107_Q	147_D	1.328	0.82
61_V	66_S	1.306	0.81
116_S	123_L	1.306	0.81
76_V	79_E	1.291	0.80
19_S	23_Q	1.288	0.80
145_A	149_K	1.282	0.79
102_L	146_T	1.28	0.79
159_N	162_A	1.275	0.79
16_D	84_E	1.273	0.79
50_E	146_T	1.271	0.78
66_S	132_A	1.256	0.77
25_T	48_L	1.238	0.76
78_M	116_S	1.23	0.75
104_A	119_T	1.223	0.75
50_E	54_Q	1.211	0.73
103_I	115_A	1.206	0.73
116_S	120_L	1.197	0.72
108_K	123_L	1.186	0.71
34_A	102_L	1.175	0.70
74_K	79_E	1.175	0.70
121_A	125_E	1.166	0.69
11_I	66_S	1.159	0.69
100_A	119_T	1.153	0.68
121_A	133_A	1.153	0.68
22_K	59_D	1.151	0.68
100_A	159_N	1.148	0.68
61_V	132_A	1.144	0.67
78_M	123_L	1.137	0.67
133_A	138_E	1.135	0.66
20_A	77_A	1.122	0.65
9_V	97_V	1.12	0.65
42_Q	46_A	1.118	0.65
74_K	77_A	1.116	0.64
121_A	141_E	1.11	0.64
24_L	109_V	1.106	0.63
92_T	98_R	1.101	0.63
59_D	62_V	1.092	0.62
78_M	108_K	1.092	0.62
47_H	143_E	1.084	0.61
54_Q	138_E	1.081	0.61
22_K	33_R	1.081	0.61
113_E	143_E	1.074	0.60
16_D	80_G	1.067	0.59
130_R	152_D	1.061	0.59
64_S	131_K	1.061	0.59
107_Q	154_A	1.059	0.58
49_E	52_H	1.055	0.58
118_G	159_N	1.044	0.57
154_A	159_N	1.038	0.56
108_K	120_L	1.034	0.56
100_A	123_L	1.032	0.56
19_S	108_K	1.024	0.55
118_G	151_T	1.022	0.54
32_A	49_E	1.02	0.54
40_L	154_A	1.016	0.54
47_H	113_E	1.015	0.54
29_A	48_L	1.014	0.54
13_L	116_S	1.013	0.53
9_V	127_L	1.009	0.53
81_L	115_A	1.006	0.53
82_I	86_N	1.004	0.52
106_A	109_V	1.001	0.52

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
2gs4A	2	1	100	0.132	Contact Map	0.447
2gyqA	2	0.994	100	0.217	Contact Map	0.645
3oghB	2	0.9759	100	0.225	Contact Map	0.373
3hiuA	4	0.9578	100	0.234	Contact Map	0.327
4etrA	2	0.9036	97.8	0.859	Contact Map	0.503
1j30A	2	0.8313	96.7	0.883	Contact Map	0.343
3uoiA	48	0.8976	95.8	0.892	Contact Map	0.383
2qqyA	1	0.8434	95.7	0.893	Contact Map	0.431
2bk6A	6	0.9036	94.8	0.899	Contact Map	0.375
2fkzA	8	0.8795	94.7	0.899	Contact Map	0.381

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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