OPENSEQ.org - 1504072123 - GREMLIN Submission

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RB1900-2100

ID:	1504072123	Query Sequence RLCSAGGADRTLFQKLKDIDTVRQAANANQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	30 (30)
Sequences:	41 (39)
Seq/Len:	1.367
Nf(neff/√len):	7.1

HHblits Results: (2016_02)
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: 1.367).

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
1_R	5_A	1.886	0.96
4_S	13_F	1.594	0.89
14_Q	22_V	1.583	0.88
8_A	16_L	1.380	0.77
22_V	25_A	1.369	0.76
12_L	16_L	1.304	0.71
6_G	14_Q	1.212	0.63
3_C	19_I	1.156	0.57
1_R	15_K	1.153	0.57
13_F	21_T	1.144	0.56
12_L	22_V	1.141	0.56
16_L	20_D	1.139	0.55
6_G	13_F	1.115	0.53
1_R	14_Q	1.068	0.48
14_Q	20_D	1.035	0.45
9_D	20_D	1.030	0.45
26_A	30_Q	1.030	0.45
1_R	30_Q	1.002	0.42

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: (06Aug15)
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
4dvyP	1	0	0.2	0.688	Contact Map
1mukA	1	0.8333	0.2	0.692	Contact Map
2o8sA	2	0.2667	0.2	0.692	Contact Map
3q23A	2	0.5667	0.2	0.701	Contact Map
2w5yA	1	0	0.2	0.715	Contact Map
4rv5A	2	0	0.2	0.715	Contact Map
1vw4S	1	0	0.2	0.715	Contact Map
3iynN	1	1	0.2	0.72	Contact Map
2xvoA	4	0.2	0.2	0.72	Contact Map
2axcA	1	0.5667	0.2	0.72	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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