OPENSEQ.org - IF3 - ECOLI GREMLIN

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IF3 - Translation initiation factor IF-3

UniProt:	P0A707	Sequence MKGGKRVQTARPNRINGEIRAQEVRLTGLEGEQLGIVSLREALEKAEEAGVDLVEISPNAEPPVCRIMDYGKFLYEKSKSSKEQKKKQKVIQVKEIKFRPGTDEGDYQVKLRSLIRFLEEGDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQELAVVESFPTKIEGRQMIMVLAPKKKQ	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10506
Length:	180 (168)
Sequences:	1195
Seq/Len:	7.11

IF3
Paralog alert: 0.02 [within 20: 0.00] - 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
107_Y	151_D	4.083	1.00
26_L	37_V	3.195	1.00
150_D	153_Q	2.939	1.00
115_I	154_E	2.881	1.00
156_A	174_L	2.763	1.00
104_E	108_Q	2.75	1.00
51_V	67_I	2.62	1.00
159_E	175_A	2.518	1.00
41_E	44_E	2.497	1.00
14_R	55_E	2.423	1.00
38_S	41_E	2.221	1.00
55_E	65_C	2.2	1.00
115_I	155_L	2.099	1.00
113_S	116_R	2.092	1.00
16_N	19_I	2.015	1.00
44_E	48_E	2.002	1.00
28_G	32_E	1.955	1.00
115_I	119_E	1.909	1.00
45_K	67_I	1.87	1.00
43_L	47_E	1.828	1.00
28_G	49_A	1.821	1.00
73_F	77_K	1.775	1.00
137_H	140_I	1.762	1.00
114_L	148_V	1.753	1.00
25_R	33_Q	1.747	1.00
143_E	146_N	1.747	1.00
142_M	146_N	1.737	1.00
23_E	61_E	1.662	1.00
29_L	49_A	1.633	1.00
45_K	49_A	1.629	1.00
44_E	47_E	1.627	1.00
114_L	126_I	1.611	1.00
21_A	39_L	1.594	1.00
130_F	170_M	1.56	1.00
24_V	65_C	1.492	0.99
105_G	108_Q	1.455	0.99
39_L	65_C	1.447	0.99
111_L	151_D	1.446	0.99
114_L	152_L	1.425	0.99
45_K	48_E	1.401	0.99
34_L	37_V	1.323	0.98
111_L	148_V	1.31	0.98
145_L	172_M	1.304	0.98
147_R	151_D	1.296	0.98
129_R	169_Q	1.282	0.97
21_A	55_E	1.253	0.97
118_L	156_A	1.247	0.97
109_V	113_S	1.224	0.96
107_Y	147_R	1.224	0.96
153_Q	177_K	1.213	0.96
123_K	173_V	1.208	0.96
130_F	141_G	1.2	0.96
135_M	168_R	1.153	0.95
108_Q	111_L	1.151	0.94
15_I	70_Y	1.138	0.94
158_V	172_M	1.136	0.94
27_T	33_Q	1.126	0.94
21_A	24_V	1.116	0.93
146_N	161_F	1.115	0.93
24_V	39_L	1.1	0.93
107_Y	111_L	1.098	0.92
128_L	145_L	1.087	0.92
149_K	172_M	1.079	0.92
160_S	173_V	1.073	0.91
97_K	129_R	1.073	0.91
135_M	138_Q	1.068	0.91
25_R	36_I	1.062	0.91
159_E	173_V	1.06	0.91
31_G	69_D	1.054	0.90
114_L	124_A	1.053	0.90
29_L	51_V	1.051	0.90
24_V	38_S	1.041	0.90
75_Y	79_K	1.031	0.89
103_D	113_S	1.028	0.89
152_L	156_A	1.02	0.88
55_E	63_P	1.017	0.88
33_Q	36_I	1.011	0.88
77_K	80_S	1.01	0.88
13_N	73_F	1.007	0.87
119_E	155_L	1.004	0.87

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
2ifeA	1	0.5556	100	0.525	Contact Map	0.721
1tifA	1	0.4333	100	0.537	Contact Map	0.769
2m71A	1	0.5222	100	0.542	Contact Map	0.741
1tigA	1	0.5167	100	0.547	Contact Map	0.797
1i96V	1	0.4889	100	0.562	Contact Map	0.035
2crqA	1	0.5556	100	0.565	Contact Map	0.637
3lhlA	1	0.4444	15	0.959	Contact Map	0.304
1pbjA	1	0.2667	14	0.96	Contact Map	0.42
2rihA	2	0.3222	11.9	0.961	Contact Map	0.606
2qrdG	2	0.3556	11.4	0.961	Contact Map	0.592

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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