OPENSEQ.org - DKSA - ECOLI GREMLIN

May 4, 2021 - We are working on upgrading the webserver, some pages may not work.

DKSA - RNA polymerase-binding transcription factor DksA

UniProt:	P0ABS1	Sequence MQEGQNRKTSSLSILAIAGVEPYQEKPGEEYMNEAQLAHFRRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10230
Length:	151 (134)
Sequences:	766
Seq/Len:	5.72

DKSA
Paralog alert: 0.10 [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
41_R	107_E	3.312	1.00
117_C	138_C	3.015	1.00
117_C	135_C	2.659	1.00
48_R	100_E	2.494	1.00
135_C	138_C	2.199	1.00
39_H	127_E	2.053	1.00
37_L	106_V	1.985	1.00
116_S	134_L	1.876	1.00
102_T	105_K	1.824	1.00
139_K	142_A	1.823	1.00
115_E	133_D	1.804	1.00
31_Y	122_G	1.79	1.00
20_V	23_Y	1.765	1.00
21_E	24_Q	1.684	1.00
32_M	40_F	1.659	1.00
24_Q	27_P	1.594	0.99
45_E	49_N	1.508	0.99
36_Q	123_I	1.472	0.99
103_L	107_E	1.464	0.99
38_A	41_R	1.457	0.99
105_K	115_E	1.425	0.98
18_A	151_G	1.396	0.98
20_V	24_Q	1.39	0.98
37_L	109_E	1.378	0.98
87_R	98_K	1.348	0.97
48_R	96_I	1.335	0.97
33_N	36_Q	1.331	0.97
49_N	53_D	1.306	0.97
104_K	108_D	1.302	0.97
48_R	52_R	1.272	0.96
98_K	129_R	1.243	0.95
90_D	93_R	1.242	0.95
38_A	45_E	1.24	0.95
111_F	132_A	1.225	0.95
50_Q	53_D	1.219	0.94
18_A	21_E	1.205	0.94
134_L	142_A	1.202	0.94
73_V	77_A	1.182	0.93
98_K	146_E	1.182	0.93
42_R	46_A	1.167	0.93
22_P	151_G	1.144	0.92
45_E	116_S	1.141	0.91
43_I	127_E	1.138	0.91
87_R	146_E	1.138	0.91
51_L	145_R	1.135	0.91
46_A	49_N	1.131	0.91
85_E	132_A	1.127	0.91
19_G	24_Q	1.126	0.91
21_E	151_G	1.125	0.91
18_A	24_Q	1.115	0.90
41_R	106_V	1.098	0.89
139_K	146_E	1.094	0.89
58_T	89_R	1.094	0.89
20_V	25_E	1.093	0.89
102_T	109_E	1.078	0.88
60_T	63_Q	1.073	0.88
32_M	39_H	1.07	0.88
113_Y	123_I	1.07	0.88
129_R	139_K	1.069	0.88
91_R	95_L	1.069	0.88
104_K	107_E	1.068	0.87
129_R	146_E	1.065	0.87
20_V	46_A	1.054	0.87
95_L	98_K	1.046	0.86
25_E	28_G	1.042	0.86
19_G	22_P	1.036	0.85
79_E	87_R	1.03	0.85
87_R	129_R	1.007	0.83
64_D	103_L	1.005	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
1tjlA	10	1	100	0.187	Contact Map	0.635
4ijjA	3	0.894	100	0.255	Contact Map	0.629
2kq9A	1	0.7417	99.9	0.356	Contact Map	0.488
2kgoA	1	0.6225	99.8	0.512	Contact Map	0.467
2lo3A	1	0.2914	40.1	0.915	Contact Map	0
2iqjA	2	0.4305	38.5	0.916	Contact Map	0.746
3u6pA	1	0.9073	36.2	0.917	Contact Map	0.417
2xzfA	1	0.9139	33.6	0.919	Contact Map	0.38
1k82A	4	0.9073	27.8	0.922	Contact Map	0.379
1d4uA	1	0.298	25.5	0.924	Contact Map	0.583

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.

Page generated in 0.013 seconds.