OPENSEQ.org - RFH - ECOLI GREMLIN

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RFH - Putative peptide chain release factor homolog

UniProt:	P28369	Sequence MLETETGRYSDTLRSALVSLDGDNAWALSESWCGTIQWICPSPYRPHHGRKNWFLGIGRFTADEQEQSDAIRYETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQENSAALKSQRRMFHHQIERGNPRRTFTGMAFIEG	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11496
Length:	166 (163)
Sequences:	2358
Seq/Len:	14.47

RFH
Paralog alert: 0.91 [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
131_Q	134_N	4.781	1.00
129_Q	133_E	3.599	1.00
133_E	137_A	3.471	1.00
77_R	90_D	2.978	1.00
76_L	105_K	2.805	1.00
130_Q	134_N	2.683	1.00
73_Y	95_A	2.668	1.00
72_R	98_L	2.491	1.00
78_S	85_H	2.419	1.00
81_P	85_H	2.295	1.00
71_I	120_R	2.292	1.00
71_I	95_A	2.245	1.00
134_N	138_L	2.22	1.00
109_E	114_A	2.129	1.00
132_Q	136_A	2.064	1.00
85_H	89_T	2.017	1.00
85_H	110_R	2	1.00
95_A	120_R	1.983	1.00
45_R	51_K	1.963	1.00
128_E	132_Q	1.963	1.00
85_H	91_S	1.951	1.00
131_Q	135_S	1.934	1.00
136_A	140_S	1.931	1.00
45_R	49_G	1.92	1.00
75_T	90_D	1.868	1.00
81_P	110_R	1.832	1.00
113_H	117_R	1.814	1.00
135_S	139_K	1.814	1.00
132_Q	135_S	1.799	1.00
4_T	13_L	1.75	1.00
117_R	121_L	1.742	1.00
109_E	118_L	1.644	1.00
96_T	103_S	1.631	1.00
1_M	16_A	1.62	1.00
122_L	126_K	1.614	1.00
108_S	118_L	1.611	1.00
78_S	88_K	1.545	1.00
97_H	100_S	1.538	1.00
85_H	88_K	1.519	1.00
74_E	96_T	1.48	1.00
136_A	139_K	1.468	1.00
97_H	101_G	1.442	1.00
161_M	164_I	1.394	0.99
72_R	96_T	1.387	0.99
33_C	58_G	1.369	0.99
92_A	107_Q	1.354	0.99
19_S	62_A	1.329	0.99
147_H	153_N	1.318	0.99
54_F	148_Q	1.314	0.99
73_Y	116_K	1.303	0.99
118_L	121_L	1.291	0.99
138_L	141_Q	1.281	0.99
140_S	144_M	1.271	0.99
124_A	128_E	1.238	0.98
102_I	130_Q	1.238	0.98
75_T	93_V	1.232	0.98
1_M	4_T	1.224	0.98
13_L	16_A	1.206	0.98
133_E	136_A	1.188	0.98
76_L	94_R	1.181	0.98
134_N	137_A	1.177	0.98
143_R	146_H	1.172	0.98
41_P	161_M	1.164	0.97
113_H	116_K	1.163	0.97
102_I	127_L	1.162	0.97
114_A	121_L	1.162	0.97
108_S	122_L	1.147	0.97
39_I	157_T	1.138	0.97
35_T	146_H	1.133	0.97
137_A	141_Q	1.12	0.96
71_I	99_A	1.115	0.96
39_I	159_T	1.11	0.96
45_R	48_H	1.09	0.96
20_L	29_S	1.078	0.95
64_E	124_A	1.074	0.95
4_T	16_A	1.073	0.95
19_S	121_L	1.069	0.95
146_H	149_I	1.066	0.95
74_E	94_R	1.05	0.94
85_H	90_D	1.039	0.94
71_I	98_L	1.014	0.93
3_E	16_A	1.003	0.93

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
2ihr1	1	0.988	100	0.074	Contact Map	0.594
1zbtA	1	0.988	100	0.074	Contact Map	0.74
3d5aX	1	0.994	100	0.078	Contact Map	0.52
2b3tB	1	0.994	100	0.085	Contact Map	0.521
1rq0A	3	0.994	100	0.09	Contact Map	0.625
1gqeA	1	0.994	100	0.099	Contact Map	0.591
2rsmA	1	0.6627	100	0.46	Contact Map	0.495
1j26A	1	0.5	99.9	0.609	Contact Map	0.403
2jvaA	1	0.506	99.9	0.616	Contact Map	0.339
4dh9Y	1	0.6205	99.9	0.619	Contact Map	0.278

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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