OPENSEQ.org - GREB - ECOLI GREMLIN

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GREB - Transcription elongation factor GreB

UniProt:	P30128	Sequence MKTPLVTREGYEKLKQELNYLWREERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCLENLKIVDYSPQQEGKVFFGAWVEIENDDGVTHRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAVVNTPAGEASWYVNAIEYVKP	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11578
Length:	158 (155)
Sequences:	2006
Seq/Len:	12.94

GREB
Paralog alert: 0.45 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: GREA GREB RNK

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
12_E	16_Q	3.535	1.00
8_R	12_E	2.96	1.00
17_E	61_R	2.701	1.00
20_Y	24_E	2.649	1.00
112_F	115_K	2.624	1.00
92_E	152_A	2.595	1.00
94_E	98_G	2.522	1.00
25_E	54_R	2.406	1.00
92_E	100_T	2.377	1.00
127_A	139_V	2.341	1.00
138_V	145_E	2.315	1.00
92_E	154_E	2.204	1.00
22_W	66_T	2.166	1.00
20_Y	25_E	2.16	1.00
57_E	60_R	2.149	1.00
19_N	23_R	2.014	1.00
108_Y	121_D	1.955	1.00
138_V	147_S	1.908	1.00
94_E	149_Y	1.901	1.00
133_V	152_A	1.891	1.00
18_L	62_V	1.89	1.00
29_V	58_I	1.865	1.00
11_Y	74_I	1.858	1.00
11_Y	15_K	1.832	1.00
67_K	71_N	1.826	1.00
92_E	102_R	1.82	1.00
26_R	59_D	1.815	1.00
131_K	137_A	1.801	1.00
25_E	28_E	1.793	1.00
136_L	147_S	1.774	1.00
21_L	58_I	1.76	1.00
93_I	101_H	1.742	1.00
94_E	100_T	1.731	1.00
84_K	132_E	1.694	1.00
136_L	149_Y	1.681	1.00
68_C	109_D	1.631	1.00
16_Q	20_Y	1.629	1.00
12_E	15_K	1.608	1.00
3_T	73_K	1.583	1.00
64_Y	68_C	1.582	1.00
140_N	145_E	1.545	1.00
85_V	150_V	1.542	1.00
93_I	148_W	1.541	1.00
102_R	154_E	1.527	1.00
50_Y	53_K	1.502	1.00
15_K	19_N	1.487	1.00
93_I	103_F	1.465	1.00
43_S	49_Q	1.458	1.00
131_K	135_D	1.396	0.99
11_Y	69_L	1.395	0.99
39_L	47_D	1.369	0.99
90_W	104_R	1.369	0.99
104_R	117_Y	1.364	0.99
133_V	153_I	1.359	0.99
33_V	55_L	1.317	0.99
10_G	110_E	1.295	0.99
28_E	31_K	1.279	0.99
37_A	42_R	1.239	0.98
9_E	117_Y	1.238	0.98
89_A	155_Y	1.237	0.98
35_W	38_S	1.224	0.98
95_N	146_A	1.22	0.98
141_T	146_A	1.213	0.98
90_W	154_E	1.212	0.98
94_E	151_N	1.204	0.98
31_K	34_T	1.169	0.97
92_E	151_N	1.164	0.97
90_W	102_R	1.16	0.97
56_R	60_R	1.133	0.97
9_E	13_K	1.126	0.97
105_I	125_A	1.111	0.96
106_V	110_E	1.067	0.95
32_K	35_W	1.065	0.95
28_E	32_K	1.062	0.95
106_V	117_Y	1.028	0.94
134_G	149_Y	1.012	0.93
88_G	107_G	1.006	0.93
14_L	65_L	1.006	0.93
35_W	39_L	1.003	0.93
7_T	10_G	1.002	0.92
9_E	104_R	1	0.92
61_R	64_Y	1	0.92

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
2p4vA	6	1	100	0.06	Contact Map	0.642
1grjA	1	0.9873	100	0.087	Contact Map	0.817
2f23A	2	0.962	100	0.139	Contact Map	0.834
2pn0A	4	0.7911	100	0.359	Contact Map	0.682
3bmbA	2	0.7911	100	0.363	Contact Map	0.703
3gtyX	1	0.8481	72.2	0.913	Contact Map	0.624
3prbA	2	0.4494	56.9	0.921	Contact Map	0.857
1wleA	2	0.9557	55.8	0.922	Contact Map	0.586
2dq3A	2	0.9494	53.8	0.923	Contact Map	0.464
1t11A	2	0.8861	52.9	0.923	Contact Map	0.612

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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