OPENSEQ.org - 1399395253 - GREMLIN Submission

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T0766 -force run

ID:	1399395253	Query Sequence MKKRVIFLLTGLFIWTSVLLAQNVPEGVIGAFKEGNSQELNKYLGDKVDLIIQNKSTHADKRTAEGTMAAFFSNHKVGSFNVNHQGKRDESGFVIGILMTANGNFRVNCFFRKVQNKYVIHQIRIDKTDE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	130 (127)
Sequences:	100 (92.2)
Seq/Len:	0.787
Nf(neff/√len):	8.2

Jackhmmer Results: (2014_04_16)
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: 0.787).

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
80_F	96_G	2.451	0.98
60_D	63_T	1.933	0.91
33_K	93_F	1.875	0.90
64_A	80_F	1.770	0.86
84_H	106_R	1.698	0.82
68_M	123_I	1.603	0.77
76_K	98_L	1.531	0.72
61_K	95_I	1.516	0.71
82_V	125_I	1.502	0.70
32_F	125_I	1.489	0.69
75_H	78_G	1.456	0.67
20_L	32_F	1.375	0.60
36_N	39_E	1.337	0.57
100_T	103_G	1.327	0.56
29_I	77_V	1.316	0.55
106_R	123_I	1.288	0.53
66_G	69_A	1.256	0.50
106_R	124_R	1.238	0.48
32_F	69_A	1.224	0.47
50_L	86_G	1.224	0.47
64_A	96_G	1.224	0.47
67_T	76_K	1.207	0.46
122_Q	125_I	1.204	0.45
53_Q	125_I	1.198	0.45
108_N	124_R	1.198	0.45
36_N	65_E	1.196	0.45
66_G	98_L	1.181	0.43
49_D	74_N	1.176	0.43
29_I	82_V	1.173	0.43
82_V	103_G	1.168	0.42
86_G	127_K	1.165	0.42
84_H	95_I	1.161	0.42
65_E	105_F	1.150	0.41
67_T	98_L	1.146	0.41
33_K	49_D	1.141	0.40
110_F	122_Q	1.138	0.40
68_M	127_K	1.138	0.40
52_I	56_S	1.137	0.40
28_V	59_A	1.129	0.39
86_G	93_F	1.122	0.39
117_K	123_I	1.113	0.38
31_A	75_H	1.103	0.37
6_I	9_L	1.102	0.37
33_K	101_A	1.101	0.37
58_H	124_R	1.101	0.37
106_R	126_D	1.093	0.36
32_F	116_N	1.090	0.36
55_K	118_Y	1.080	0.35
98_L	110_F	1.079	0.35
24_V	107_V	1.078	0.35
12_L	117_K	1.077	0.35
87_K	93_F	1.071	0.34
60_D	67_T	1.069	0.34
78_G	105_F	1.067	0.34
64_A	125_I	1.053	0.33
35_G	64_A	1.050	0.33
18_V	48_V	1.045	0.32
44_L	77_V	1.039	0.32
59_A	63_T	1.037	0.32
70_A	85_Q	1.036	0.32
7_F	62_R	1.027	0.31
44_L	66_G	1.024	0.31
37_S	65_E	1.020	0.31
80_F	125_I	1.019	0.30
49_D	118_Y	1.018	0.30
84_H	125_I	1.018	0.30
55_K	70_A	1.015	0.30
31_A	85_Q	1.012	0.30
107_V	118_Y	1.009	0.30

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
4orlA	1	0.8462	100	0.165	Contact Map
4q53A	2	0.8385	100	0.168	Contact Map
3f7sA	1	0.9154	90.3	0.883	Contact Map
3h51A	2	0.9385	87.1	0.889	Contact Map
3gwrA	2	0.8923	86.4	0.891	Contact Map
3bb9A	6	0.8	85.9	0.891	Contact Map
4fczB	2	0.8538	85.9	0.891	Contact Map
4u13A	2	0.8231	85.9	0.891	Contact Map
3d9rA	4	0.9308	85.7	0.892	Contact Map
3ff2A	1	0.8308	84	0.894	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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