OPENSEQ.org - 1406136844 - GREMLIN Submission

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T0827 212-369 -force run

ID:	1406136844	Query Sequence VSREILQDAVGDVFALASAEGWQDPLSRKALQFIERRQRNRAAIAKSPFNSLDEAVAAGEGGFNREIAEEISYLSGLKPMTGAKIFTDPGGEPLAILCKATGLPRGCVRQLWRGLRRQEVDRTGATDPNLERVLTVYDAIAVDRAQTVLRYWNWSLTS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	158 (157)
Sequences:	94 (65.4)
Seq/Len:	0.599
Nf(neff/√len):	5.2

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: 0.599).

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
95_A	108_V	1.752	0.79
43_A	47_S	1.577	0.67
58_A	90_G	1.517	0.63
101_T	139_A	1.449	0.58
39_R	92_E	1.428	0.56
96_I	148_V	1.395	0.53
85_I	107_C	1.369	0.51
98_C	150_R	1.342	0.49
58_A	105_R	1.334	0.49
147_T	151_Y	1.319	0.47
31_L	95_A	1.313	0.47
124_G	137_Y	1.278	0.44
15_A	137_Y	1.262	0.43
102_G	143_D	1.250	0.42
38_Q	111_L	1.236	0.41
37_R	132_R	1.233	0.41
31_L	39_R	1.233	0.41
98_C	101_T	1.227	0.40
88_D	95_A	1.222	0.40
99_K	149_L	1.221	0.40
111_L	128_P	1.219	0.39
4_E	139_A	1.218	0.39
2_S	7_Q	1.210	0.39
115_L	151_Y	1.204	0.38
5_I	9_A	1.202	0.38
59_G	108_V	1.202	0.38
78_K	98_C	1.200	0.38
10_V	14_F	1.197	0.38
99_K	139_A	1.196	0.38
41_R	82_G	1.194	0.37
103_L	108_V	1.189	0.37
101_T	130_L	1.189	0.37
92_E	147_T	1.187	0.37
31_L	149_L	1.185	0.37
58_A	108_V	1.178	0.36
62_G	93_P	1.177	0.36
88_D	152_W	1.177	0.36
149_L	153_N	1.167	0.35
74_L	113_R	1.151	0.34
125_A	137_Y	1.151	0.34
113_R	137_Y	1.150	0.34
68_A	152_W	1.150	0.34
86_F	150_R	1.147	0.34
31_L	36_R	1.142	0.34
85_I	110_Q	1.140	0.33
111_L	129_N	1.139	0.33
47_S	137_Y	1.133	0.33
31_L	37_R	1.133	0.33
58_A	95_A	1.132	0.33
94_L	138_D	1.125	0.32
77_L	150_R	1.125	0.32
29_K	56_V	1.124	0.32
95_A	138_D	1.122	0.32
2_S	96_I	1.113	0.32
7_Q	143_D	1.112	0.32
5_I	121_D	1.111	0.31
90_G	95_A	1.110	0.31
30_A	143_D	1.102	0.31
53_D	81_T	1.101	0.31
4_E	155_S	1.097	0.30
103_L	146_Q	1.096	0.30
74_L	150_R	1.092	0.30
52_L	70_E	1.091	0.30
68_A	124_G	1.091	0.30
14_F	101_T	1.082	0.29
15_A	19_A	1.078	0.29
59_G	71_I	1.077	0.29
115_L	120_V	1.069	0.29
72_S	84_K	1.069	0.29
2_S	10_V	1.064	0.28
83_A	98_C	1.063	0.28
118_Q	157_T	1.060	0.28
2_S	11_G	1.055	0.28
18_S	75_S	1.054	0.28
88_D	92_E	1.052	0.27
79_P	85_I	1.050	0.27
95_A	105_R	1.049	0.27
33_F	98_C	1.049	0.27
13_V	20_E	1.049	0.27
101_T	150_R	1.047	0.27
137_Y	142_V	1.045	0.27
41_R	60_E	1.045	0.27
96_I	112_W	1.042	0.27
31_L	92_E	1.036	0.26
20_E	24_D	1.035	0.26
67_I	103_L	1.033	0.26
57_A	110_Q	1.031	0.26
63_F	138_D	1.029	0.26
34_I	71_I	1.028	0.26
4_E	157_T	1.023	0.26
59_G	66_E	1.021	0.26
58_A	92_E	1.013	0.25
93_P	104_P	1.010	0.25
10_V	107_C	1.005	0.25

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: (12Jul14)
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
3pxpA	3	0.7089	68.2	0.915	Contact Map
3op9A	1	0.6392	48.3	0.925	Contact Map
1b0nA	1	0.6139	44.6	0.926	Contact Map
3qwgA	2	0.462	43.9	0.927	Contact Map
3ivpA	4	0.6709	36.2	0.93	Contact Map
4o8bA	1	0.5823	36	0.93	Contact Map
4jcyA	2	0.538	29.7	0.933	Contact Map
2ppxA	1	0.3608	28.5	0.934	Contact Map
2of5A	7	0.4114	26.6	0.935	Contact Map
2o71A	1	0.4114	26.6	0.935	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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