OPENSEQ.org - YCDY - ECOLI GREMLIN

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YCDY - Chaperone protein YcdY

UniProt:	P75915	Sequence MNEFSILCRVLGSLYYRQPQDPLLVPLFTLIREGKLAANWPLEQDELLTRLQKSCDMTQVSADYNALFIGDECAVPPYRSAWVEGATEAEVRAFLSERGMPLADTPADHIGTLLLAASWLEDQSTEDESEALETLFSEYLLPWCGAFLGKVEAHATTPFWRTMAPLTRDAISAMWDELEEDSEE	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13871
Length:	184 (180)
Sequences:	601
Seq/Len:	3.34

YCDY
Paralog alert: 0.80 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: DMSD TORD YCDY

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
95_L	116_A	3.153	1.00
63_D	157_T	2.876	1.00
92_R	107_A	2.863	1.00
15_Y	167_T	2.646	1.00
110_I	144_C	2.61	1.00
152_E	168_R	2.248	1.00
147_F	151_V	2.213	1.00
91_V	95_L	1.904	1.00
21_D	25_V	1.85	0.99
79_R	83_V	1.826	0.99
8_C	170_A	1.819	0.99
152_E	165_P	1.799	0.99
16_Y	111_G	1.788	0.99
15_Y	110_I	1.781	0.99
65_N	69_I	1.748	0.99
79_R	91_V	1.728	0.99
63_D	155_A	1.698	0.99
100_M	119_W	1.68	0.99
8_C	174_M	1.56	0.97
144_C	171_I	1.551	0.97
144_C	148_L	1.526	0.97
12_G	115_L	1.517	0.97
148_L	167_T	1.497	0.96
82_W	150_K	1.453	0.96
60_V	159_F	1.418	0.95
155_A	158_P	1.411	0.95
118_S	122_D	1.4	0.94
117_A	170_A	1.369	0.93
91_V	113_L	1.368	0.93
77_P	106_P	1.367	0.93
10_V	14_L	1.342	0.92
49_T	53_K	1.335	0.92
113_L	116_A	1.319	0.92
176_D	179_E	1.315	0.91
79_R	113_L	1.302	0.91
8_C	117_A	1.295	0.91
151_V	164_A	1.286	0.90
14_L	159_F	1.268	0.89
164_A	167_T	1.262	0.89
11_L	159_F	1.248	0.88
9_R	122_D	1.247	0.88
4_F	42_L	1.219	0.87
113_L	135_L	1.205	0.86
55_C	60_V	1.202	0.86
76_P	81_A	1.188	0.85
158_P	161_R	1.186	0.85
76_P	79_R	1.174	0.84
117_A	174_M	1.164	0.83
11_L	167_T	1.161	0.83
63_D	66_A	1.156	0.82
23_L	166_L	1.139	0.81
117_A	132_L	1.135	0.81
13_S	17_R	1.123	0.80
12_G	111_G	1.111	0.79
84_E	87_T	1.111	0.79
78_Y	88_E	1.111	0.79
10_V	132_L	1.111	0.79
148_L	164_A	1.098	0.78
69_I	73_C	1.096	0.78
88_E	107_A	1.09	0.77
14_L	163_M	1.089	0.77
10_V	135_L	1.086	0.77
81_A	88_E	1.081	0.76
69_I	109_H	1.075	0.76
73_C	77_P	1.074	0.76
41_P	110_I	1.061	0.74
8_C	132_L	1.056	0.74
8_C	115_L	1.047	0.73
11_L	91_V	1.044	0.73
15_Y	163_M	1.039	0.72
145_G	168_R	1.036	0.72
70_G	73_C	1.031	0.71
16_Y	112_T	1.02	0.70
135_L	142_P	1.017	0.70
103_A	169_D	1.015	0.70
9_R	118_S	1.013	0.69
79_R	139_Y	1.01	0.69
26_P	114_L	1.005	0.68
155_A	161_R	1.002	0.68
10_V	27_L	1.002	0.68

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
1s9uA	1	0.9783	100	0.207	Contact Map	0.642
1n1cA	2	0.962	100	0.243	Contact Map	0.593
2o9xA	1	0.837	100	0.353	Contact Map	0.611
2xolA	2	0.8043	100	0.398	Contact Map	0.655
1g03A	1	0.3967	3.5	0.954	Contact Map	0.532
2ra9A	1	0.3043	3.2	0.955	Contact Map	0.157
2nn4A	3	0.3859	2.5	0.958	Contact Map	0.484
3ewtE	1	0.1141	2.2	0.959	Contact Map	0
3er9B	1	0.3152	1.9	0.96	Contact Map	0.23
2aq4A	1	0.3478	1.4	0.964	Contact Map	0.202

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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