OPENSEQ.org - NRDG - ECOLI GREMLIN

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

NRDG - Anaerobic ribonucleoside-triphosphate reductase-activating protein

UniProt:	P0A9N8	Sequence MNYHQYYPVDIVNGPGTRCTLFVSGCVHECPGCYNKSTWRVNSGQPFTKAMEDQIINDLNDTRIKRQGISLSGGDPLHPQNVPDILKLVQRIRAECPGKDIWVWTGYKLDELNAAQMQVVDLINVLVDGKFVQDLKDPSLIWRGSSNQVVHHLR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12523
Length:	154 (151)
Sequences:	2117
Seq/Len:	14.02

NRDG
Paralog alert: 0.78 [within 20: 0.02] - ratio of genomes with paralogs
Cluster includes: NRDG PFLA PFLC PFLE YJJW

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
69_I	92_I	3.534	1.00
60_N	95_E	3.357	1.00
71_L	85_I	3.047	1.00
4_H	38_T	2.854	1.00
90_Q	122_L	2.534	1.00
90_Q	118_Q	2.351	1.00
53_D	91_R	2.299	1.00
91_R	94_A	2.27	1.00
134_D	148_Q	2.253	1.00
91_R	95_E	2.155	1.00
71_L	89_V	2.153	1.00
134_D	146_S	2.142	1.00
106_G	127_V	2.033	1.00
89_V	101_I	1.986	1.00
27_V	105_T	1.942	1.00
135_L	146_S	1.851	1.00
86_L	118_Q	1.814	1.00
19_C	58_D	1.767	1.00
52_E	91_R	1.766	1.00
49_K	53_D	1.756	1.00
27_V	78_H	1.744	1.00
93_R	124_N	1.742	1.00
14_G	68_G	1.705	1.00
59_L	92_I	1.652	1.00
66_R	103_V	1.644	1.00
2_N	46_P	1.624	1.00
14_G	18_R	1.596	1.00
56_I	91_R	1.583	1.00
103_V	123_I	1.552	1.00
83_P	115_A	1.508	1.00
117_M	121_D	1.502	1.00
7_Y	10_D	1.455	1.00
27_V	107_Y	1.438	1.00
41_V	78_H	1.435	1.00
77_L	103_V	1.427	1.00
71_L	88_L	1.416	1.00
137_D	146_S	1.412	1.00
18_R	70_S	1.386	0.99
93_R	122_L	1.386	0.99
3_Y	23_V	1.371	0.99
102_W	125_V	1.352	0.99
67_Q	100_D	1.334	0.99
56_I	92_I	1.294	0.99
6_Y	19_C	1.288	0.99
18_R	68_G	1.277	0.99
148_Q	152_H	1.277	0.99
29_E	39_W	1.233	0.98
118_Q	121_D	1.219	0.98
76_P	85_I	1.214	0.98
53_D	57_N	1.209	0.98
132_V	135_L	1.204	0.98
90_Q	94_A	1.2	0.98
1_M	84_D	1.197	0.98
28_H	107_Y	1.196	0.98
49_K	91_R	1.187	0.98
133_Q	136_K	1.185	0.98
13_N	34_Y	1.178	0.98
10_D	20_T	1.168	0.97
2_N	43_S	1.166	0.97
131_F	136_K	1.164	0.97
147_N	150_V	1.163	0.97
77_L	119_V	1.132	0.97
3_Y	21_L	1.113	0.96
86_L	90_Q	1.098	0.96
86_L	122_L	1.082	0.96
109_L	153_L	1.079	0.95
56_I	60_N	1.078	0.95
21_L	55_I	1.077	0.95
20_T	72_S	1.075	0.95
85_I	89_V	1.072	0.95
89_V	123_I	1.066	0.95
34_Y	72_S	1.065	0.95
131_F	142_W	1.064	0.95
108_K	111_E	1.038	0.94
8_P	58_D	1.033	0.94
23_V	76_P	1.009	0.93
59_L	88_L	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
3c8fA	1	0.9221	99.9	0.493	Contact Map	0.694
2yx0A	1	0.9091	99.6	0.652	Contact Map	0.615
1tv8A	2	0.8831	99.4	0.706	Contact Map	0.635
3rfaA	2	0.8831	99.3	0.711	Contact Map	0.458
2z2uA	1	0.8961	99.3	0.711	Contact Map	0.693
4k36A	2	0.8571	99.2	0.726	Contact Map	0.513
2qgqA	8	0.8312	99.1	0.735	Contact Map	0.682
3canA	1	0.539	99.1	0.737	Contact Map	0.643
1oltA	1	0.9416	99.1	0.742	Contact Map	0.524
4m7tA	1	0.9416	99	0.747	Contact Map	0.642

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 0.8148 seconds.