OPENSEQ.org - 1490918156 - GREMLIN Submission

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BfmS_30-240_dom1

ID:	1490918156	Query Sequence QIINYQRAQEYRESLTDGISYVISEGVARQPGKQQKIDWISDASDLLELPIYYTDASKVELSRTEKKRIEAQKSVVRYDASNSIAYVIIGLRDDPQHYLSIKVD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	104 (104)
Sequences:	267 (171.5)
Seq/Len:	2.567
Nf(neff/√len):	16.8

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: 2.567).

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
49_L	101_I	2.213	1.00
15_L	47_L	1.848	0.99
85_A	103_V	1.724	0.98
7_R	11_Y	1.695	0.98
4_N	7_R	1.661	0.97
9_Q	44_S	1.628	0.97
84_I	103_V	1.614	0.97
68_R	99_L	1.491	0.94
6_Q	68_R	1.408	0.91
83_S	103_V	1.398	0.91
19_I	22_V	1.335	0.88
13_E	24_S	1.303	0.86
83_S	104_D	1.289	0.86
59_V	98_Y	1.271	0.84
89_I	101_I	1.260	0.84
33_K	83_S	1.237	0.82
5_Y	62_S	1.230	0.82
56_A	98_Y	1.229	0.82
4_N	20_S	1.219	0.81
92_R	95_P	1.204	0.80
55_D	58_K	1.202	0.80
36_K	85_A	1.199	0.79
44_S	57_S	1.194	0.79
38_D	42_D	1.193	0.79
4_N	18_G	1.191	0.79
3_I	17_D	1.176	0.78
13_E	68_R	1.173	0.77
8_A	91_L	1.172	0.77
5_Y	57_S	1.172	0.77
7_R	39_W	1.164	0.77
7_R	68_R	1.161	0.76
26_G	71_A	1.149	0.75
61_L	65_E	1.146	0.75
21_Y	89_I	1.142	0.75
7_R	46_L	1.132	0.74
47_L	98_Y	1.120	0.73
12_R	16_T	1.120	0.73
18_G	48_E	1.117	0.72
1_Q	51_I	1.110	0.72
4_N	46_L	1.107	0.71
84_I	104_D	1.104	0.71
13_E	16_T	1.086	0.69
48_E	100_S	1.086	0.69
66_K	83_S	1.084	0.69
17_D	89_I	1.081	0.69
7_R	13_E	1.079	0.69
88_I	92_R	1.077	0.68
43_A	50_P	1.071	0.68
32_G	58_K	1.071	0.68
66_K	93_D	1.064	0.67
18_G	61_L	1.061	0.67
2_I	53_Y	1.057	0.66
56_A	90_G	1.036	0.64
69_I	73_K	1.029	0.63
86_Y	100_S	1.021	0.62
39_W	91_L	1.012	0.61
5_Y	48_E	1.010	0.61
7_R	16_T	1.006	0.61
9_Q	14_S	1.006	0.61
75_V	81_S	1.005	0.60

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
2io8A	2	0.8654	2.9	0.918	Contact Map
2vobA	2	0.8654	2.6	0.92	Contact Map
1q42A	1	0.5769	2	0.925	Contact Map
4alzA	1	0.5192	2	0.925	Contact Map
2f8mA	2	0.8365	1.9	0.926	Contact Map
2au3A	1	0.5577	1.8	0.927	Contact Map
2va8A	2	0.4904	1.8	0.927	Contact Map
1m22A	2	0.9135	1.8	0.927	Contact Map
3kfuE	2	0.8462	1.7	0.928	Contact Map
3h0lA	8	0.8846	1.6	0.929	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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