OPENSEQ.org - LIGT - ECOLI GREMLIN

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LIGT - 2'-5'-RNA ligase

UniProt:	P37025	Sequence MSEPQRLFFAIDLPAEIREQIIHWRATHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12330
Length:	176 (172)
Sequences:	1001
Seq/Len:	5.82

LIGT
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
80_G	89_W	3.809	1.00
72_F	149_V	3.682	1.00
47_A	107_R	3.234	1.00
151_E	171_R	3.073	1.00
153_T	168_P	3.016	1.00
80_G	91_G	2.942	1.00
158_S	167_T	2.901	1.00
21_I	90_L	2.662	1.00
156_A	167_T	2.612	1.00
9_F	64_A	2.584	1.00
12_D	155_Y	2.529	1.00
60_L	110_A	2.24	1.00
34_G	129_L	2.182	1.00
10_A	155_Y	2.098	1.00
159_F	164_T	2.096	1.00
7_L	52_V	2.084	1.00
152_F	172_W	1.912	1.00
9_F	49_L	1.901	1.00
9_F	106_L	1.881	1.00
67_I	152_F	1.861	1.00
47_A	117_Q	1.856	1.00
64_A	106_L	1.801	1.00
11_I	149_V	1.799	1.00
160_A	163_R	1.693	1.00
156_A	169_L	1.677	1.00
155_Y	168_P	1.617	0.99
41_N	157_S	1.603	0.99
76_L	90_L	1.583	0.99
160_A	165_R	1.58	0.99
168_P	171_R	1.53	0.99
49_L	115_C	1.522	0.99
37_V	164_T	1.517	0.99
14_P	17_I	1.456	0.99
14_P	147_Y	1.445	0.99
25_R	42_L	1.437	0.98
46_L	152_F	1.436	0.98
65_G	170_K	1.425	0.98
5_Q	51_E	1.425	0.98
53_S	56_K	1.42	0.98
159_F	163_R	1.394	0.98
103_A	107_R	1.373	0.98
49_L	110_A	1.347	0.97
69_Q	174_L	1.344	0.97
37_V	130_R	1.343	0.97
77_D	93_R	1.336	0.97
41_N	166_Y	1.332	0.97
82_W	91_G	1.311	0.97
6_R	157_S	1.303	0.97
153_T	171_R	1.257	0.96
7_L	154_L	1.246	0.95
73_T	148_A	1.237	0.95
82_W	89_W	1.206	0.94
5_Q	156_A	1.196	0.94
7_L	49_L	1.183	0.93
118_S	122_F	1.18	0.93
90_L	128_L	1.156	0.92
21_I	128_L	1.151	0.92
130_R	164_T	1.149	0.92
19_E	39_A	1.129	0.91
38_A	41_N	1.112	0.90
47_A	115_C	1.103	0.90
6_R	130_R	1.086	0.89
11_I	72_F	1.083	0.89
74_L	149_V	1.066	0.88
107_R	117_Q	1.064	0.88
44_L	70_P	1.042	0.86
76_L	126_I	1.042	0.86
36_P	129_L	1.042	0.86
78_D	92_M	1.037	0.86
74_L	99_L	1.031	0.85
13_L	18_R	1.027	0.85
13_L	155_Y	1.025	0.85
106_L	110_A	1.02	0.84
18_R	39_A	1.019	0.84
6_R	51_E	1.009	0.83
130_R	163_R	1.001	0.83
61_S	170_K	1	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
1iuhA	1	0.9602	100	0.229	Contact Map	0.656
1vgjA	1	0.9659	100	0.253	Contact Map	0.772
3j4qA	1	0.9943	100	0.266	Contact Map	0.647
2vfkA	1	0.983	100	0.302	Contact Map	0.659
4h7wA	1	0.9261	100	0.372	Contact Map	0.409
1jh6A	2	0.9375	100	0.379	Contact Map	0.643
2d4gA	2	0.9091	100	0.38	Contact Map	0.762
2fsqA	1	0.9205	96.7	0.848	Contact Map	0.414
1zpwX	1	0.4943	14.9	0.939	Contact Map	0.391
3oq2A	2	0.517	14.8	0.939	Contact Map	0.518

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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