OPENSEQ.org - 1484028985 - GREMLIN Submission

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HRG1 -force run

ID:	1484028985	Query Sequence MAPSRLQLGLRAAYSGISSVAGFSIFLVWTVVYRQPGTAAMGGLAGVLALWVLVTHVMYMQDYWRTWLKGLRGFFFVGVLFSAVSIAAFCTFLVLAITRHQSLTDPTSYYLSSVWSFISFKWAFLLSLYAHRYRADFADISILSDF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	146 (145)
Sequences:	94 (65.1)
Seq/Len:	0.648
Nf(neff/√len):	5.4

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: 0.648).

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
18_S	45_A	1.800	0.83
82_S	120_F	1.764	0.81
56_H	133_Y	1.635	0.74
12_A	53_L	1.555	0.68
86_I	95_L	1.497	0.64
115_W	121_K	1.487	0.63
95_L	101_Q	1.469	0.62
74_F	81_F	1.439	0.59
18_S	25_I	1.427	0.58
35_Q	38_T	1.399	0.56
26_F	126_L	1.385	0.55
35_Q	49_A	1.360	0.53
86_I	94_V	1.359	0.53
24_S	86_I	1.358	0.53
90_C	131_H	1.358	0.53
31_V	88_A	1.352	0.52
75_F	87_A	1.351	0.52
71_L	126_L	1.339	0.51
79_V	109_Y	1.308	0.49
88_A	100_H	1.295	0.48
90_C	100_H	1.294	0.48
24_S	121_K	1.269	0.46
22_G	45_A	1.263	0.45
29_W	35_Q	1.262	0.45
91_T	94_V	1.261	0.45
20_V	120_F	1.255	0.44
83_A	90_C	1.245	0.44
13_A	137_F	1.243	0.43
65_R	123_A	1.232	0.43
46_G	78_G	1.229	0.42
23_F	113_S	1.211	0.41
41_M	92_F	1.196	0.40
21_A	83_A	1.195	0.40
50_L	55_T	1.192	0.39
18_S	118_I	1.180	0.38
115_W	118_I	1.174	0.38
45_A	118_I	1.173	0.38
75_F	90_C	1.172	0.38
80_L	83_A	1.171	0.38
18_S	49_A	1.164	0.37
115_W	133_Y	1.162	0.37
6_L	100_H	1.159	0.37
52_V	101_Q	1.158	0.37
94_V	98_T	1.145	0.36
75_F	123_A	1.144	0.36
10_L	17_I	1.141	0.35
55_T	88_A	1.136	0.35
50_L	145_D	1.132	0.35
18_S	22_G	1.130	0.35
18_S	35_Q	1.121	0.34
56_H	121_K	1.112	0.33
71_L	78_G	1.111	0.33
16_G	131_H	1.090	0.32
33_Y	60_M	1.088	0.31
8_L	72_R	1.075	0.31
117_F	125_L	1.072	0.30
142_I	145_D	1.071	0.30
93_L	115_W	1.070	0.30
24_S	115_W	1.070	0.30
29_W	42_G	1.069	0.30
62_D	74_F	1.066	0.30
53_L	58_M	1.062	0.30
26_F	45_A	1.056	0.29
53_L	90_C	1.050	0.29
31_V	109_Y	1.041	0.28
15_S	125_L	1.040	0.28
141_S	145_D	1.040	0.28
12_A	17_I	1.038	0.28
72_R	78_G	1.038	0.28
12_A	40_A	1.032	0.28
15_S	102_S	1.025	0.27
9_G	29_W	1.022	0.27
16_G	83_A	1.013	0.26
75_F	79_V	1.012	0.26
20_V	125_L	1.009	0.26
75_F	130_A	1.003	0.26
50_L	72_R	1.000	0.26
23_F	76_F	1.000	0.26

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
4p79A	1	0.6781	11.2	0.947	Contact Map
3x29A	2	0.6096	4	0.957	Contact Map
3b9wA	1	0.8836	2.9	0.959	Contact Map
4ev6A	5	0.4041	2.9	0.959	Contact Map
3ixzA	1	0.9589	2.9	0.959	Contact Map
4x5mA	3	0.6164	2.8	0.96	Contact Map
4uvmA	1	0.5548	2.3	0.962	Contact Map
3j1zP	2	0.9795	2.2	0.962	Contact Map
4gx0A	4	0.4247	2	0.963	Contact Map
4qndA	1	0.6233	1.9	0.963	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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