OPENSEQ.org - 1415824216 - GREMLIN Submission

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4J8T_A -force run

ID:	1415824216	Query Sequence MNAKEIVVHALRLLENGDARGWCDLFHPEGVLEYPYPPPGYKTRFEGRETIWAHMRLFPEYMTIRFTDVQFYETADPDLAIGEFHGDGVHTVSGGKLAADYISVLRTRDGQILLYRLFFNPLRVLEPLGLE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	131 (129)
Sequences:	119 (112.7)
Seq/Len:	0.922
Nf(neff/√len):	9.9

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: 0.922).

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
36_Y	99_A	2.301	0.98
30_G	51_I	2.005	0.95
34_Y	119_F	1.941	0.94
104_V	117_L	1.813	0.90
33_E	44_R	1.708	0.86
51_I	82_G	1.578	0.80
79_L	106_R	1.548	0.78
101_Y	119_F	1.520	0.76
11_L	111_Q	1.466	0.72
78_D	108_R	1.465	0.72
25_L	82_G	1.406	0.68
9_H	13_L	1.392	0.66
84_F	101_Y	1.391	0.66
54_H	119_F	1.352	0.63
6_I	70_Q	1.324	0.61
22_W	105_L	1.323	0.61
6_I	107_T	1.312	0.60
45_F	118_F	1.305	0.59
83_E	116_R	1.297	0.58
90_H	128_L	1.294	0.58
54_H	115_Y	1.278	0.57
84_F	115_Y	1.261	0.55
108_R	113_L	1.254	0.54
48_R	74_T	1.254	0.54
28_P	49_E	1.252	0.54
109_D	126_E	1.244	0.54
106_R	113_L	1.240	0.53
28_P	46_E	1.239	0.53
46_E	50_T	1.238	0.53
74_T	77_P	1.237	0.53
84_F	117_L	1.231	0.52
5_E	109_D	1.222	0.52
76_D	126_E	1.209	0.50
37_P	118_F	1.199	0.50
18_D	21_G	1.195	0.49
63_T	117_L	1.193	0.49
8_V	82_G	1.182	0.48
94_G	127_P	1.175	0.47
27_H	36_Y	1.157	0.46
115_Y	121_P	1.152	0.45
38_P	120_N	1.151	0.45
28_P	81_I	1.149	0.45
51_I	84_F	1.141	0.44
48_R	56_R	1.127	0.43
16_N	78_D	1.124	0.43
54_H	121_P	1.103	0.41
10_A	22_W	1.103	0.41
71_F	120_N	1.099	0.41
72_Y	75_A	1.090	0.40
28_P	53_A	1.089	0.40
26_F	82_G	1.087	0.39
26_F	51_I	1.082	0.39
96_K	119_F	1.075	0.38
35_P	121_P	1.072	0.38
36_Y	73_E	1.059	0.37
22_W	58_F	1.054	0.37
36_Y	81_I	1.048	0.36
22_W	66_F	1.048	0.36
24_D	44_R	1.043	0.36
65_R	105_L	1.043	0.36
35_P	104_V	1.042	0.36
25_L	66_F	1.039	0.35
5_E	92_V	1.037	0.35
38_P	68_D	1.025	0.34
10_A	55_M	1.024	0.34
64_I	88_G	1.023	0.34
34_Y	117_L	1.020	0.34
30_G	111_Q	1.006	0.33
31_V	76_D	1.005	0.33

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

See coupling matrix (for protein design or mutagenesis)
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: (06Sep14)
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
1s5aA	4	1	99.9	0.522	Contact Map
1z1sA	1	0.9847	99.9	0.529	Contact Map
3jumA	2	0.9924	99.8	0.559	Contact Map
3ff0A	2	0.9924	99.8	0.562	Contact Map
3grdA	2	0.9695	99.8	0.576	Contact Map
3dm8A	1	0.9847	99.8	0.581	Contact Map
3dmcA	2	0.9237	99.8	0.593	Contact Map
2a15A	1	0.9313	99.8	0.595	Contact Map
3fgyA	2	0.9847	99.8	0.597	Contact Map
3ebtA	1	0.9771	99.8	0.605	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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