OPENSEQ.org - 1437447025 - GREMLIN Submission

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ID:	1437447025	Query Sequence YPEGVRFGEEEDDIARLVIGIAARNNEHIQVITSLTNALDDESVIERLAHTTSVDEVLELLAGRKLFKLGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTPTYLGESIAVPHGTVEAKDRVLKTGVVFCQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	145 (133)
Sequences:	470 (329.7)
Seq/Len:	3.534
Nf(neff/√len):	28.6

HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 3.534).

Sequences per length for each position, AFTER the coverage/gap filter was applied

Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

i	j	Scaled score	Prob
20_G	23_A	2.231	1.00
75_F	89_F	2.177	1.00
88_R	105_V	2.034	1.00
80_A	89_F	1.841	0.99
90_A	142_V	1.616	0.98
104_Y	108_M	1.591	0.98
124_A	127_H	1.575	0.98
117_T	126_P	1.565	0.98
17_L	143_F	1.538	0.97
111_R	117_T	1.512	0.97
111_R	126_P	1.458	0.96
117_T	139_T	1.406	0.95
39_L	125_V	1.402	0.95
16_R	45_I	1.398	0.95
139_T	144_C	1.394	0.95
110_D	113_K	1.392	0.95
94_L	100_V	1.389	0.95
19_I	34_S	1.384	0.94
99_Y	140_G	1.351	0.93
103_E	110_D	1.346	0.93
111_R	127_H	1.339	0.93
83_K	126_P	1.337	0.93
105_V	109_L	1.283	0.91
39_L	114_L	1.281	0.91
112_E	117_T	1.278	0.91
16_R	37_N	1.234	0.89
90_A	143_F	1.233	0.88
100_V	104_Y	1.230	0.88
22_A	29_I	1.225	0.88
47_R	141_V	1.208	0.87
78_R	89_F	1.199	0.87
91_G	105_V	1.196	0.86
87_I	127_H	1.178	0.85
37_N	40_D	1.177	0.85
121_E	125_V	1.167	0.84
39_L	130_V	1.152	0.83
119_L	136_V	1.152	0.83
21_I	29_I	1.150	0.83
92_E	98_G	1.140	0.83
86_A	144_C	1.134	0.82
119_L	130_V	1.128	0.82
115_T	118_Y	1.128	0.82
15_A	18_V	1.127	0.82
28_H	142_V	1.124	0.81
92_E	96_K	1.123	0.81
119_L	125_V	1.122	0.81
92_E	105_V	1.121	0.81
46_E	142_V	1.116	0.81
112_E	124_A	1.111	0.80
17_L	29_I	1.103	0.80
72_E	97_G	1.088	0.78
94_L	99_Y	1.088	0.78
22_A	34_S	1.084	0.78
64_R	82_T	1.077	0.77
78_R	128_G	1.076	0.77
107_A	132_A	1.072	0.77
96_K	139_T	1.064	0.76
112_E	127_H	1.057	0.75
82_T	85_E	1.055	0.75
104_Y	136_V	1.048	0.75
86_A	104_Y	1.045	0.74
82_T	86_A	1.038	0.74
69_L	131_E	1.031	0.73
74_I	91_G	1.028	0.73
78_R	144_C	1.028	0.73
59_E	63_G	1.026	0.72
87_I	126_P	1.025	0.72
83_K	125_V	1.025	0.72
87_I	91_G	1.024	0.72
87_I	124_A	1.024	0.72
15_A	43_S	1.022	0.72
93_Q	139_T	1.021	0.72
40_D	77_G	1.016	0.71
130_V	136_V	1.012	0.71
91_G	108_M	1.010	0.71
24_R	97_G	1.009	0.71
94_L	139_T	1.008	0.70
104_Y	126_P	1.003	0.70

Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).

Text file of contact predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

NEW Features

Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.

HHsearch Results: (31Jan15)
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-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.

PDB	M	Cov	P(%)	HHΔ
1a3aA	4	0.5586	99.7	0.543	Contact Map
1a6jA	2	0.6	99.7	0.546	Contact Map
4m62S	2	0.5586	99.6	0.55	Contact Map
2a0jA	1	0.5517	99.6	0.562	Contact Map
3bjvA	1	0.5655	99.6	0.565	Contact Map
3oxpA	2	0.5517	99.6	0.567	Contact Map
3urrA	2	0.5655	99.6	0.569	Contact Map
2oqtA	4	0.5724	99.6	0.574	Contact Map
2oq3A	1	0.5586	99.6	0.575	Contact Map
3t43A	2	0.4276	99.5	0.592	Contact Map

M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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