OPENSEQ.org - 1406831374 - GREMLIN Submission

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T0834 2-215 -force run

ID:	1406831374	Query Sequence SLPERIDLFVSLFDYNSATTSYDIRSIQTDFPTRLLTPDSMLPQTSEYPLKDIQLLYKLAQSCTGKLPLSPLITEPLVFTRSLCKGSSLSPRWFARSGLIHPGGGTYAFRYAEKYPAQFANLLPYMHIQERPNAAEGTLLYHLQNMGEDAINALVSGASMFGSGSDLWLRKGDIYYLFNEETWLTNANKAGLSYSLLSADNTCFIQRGNICWDV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	214 (213)
Sequences:	61 (52.3)
Seq/Len:	0.286
Nf(neff/√len):	3.6

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: 0.286).

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_L	88_S	1.784	0.59
57_Y	122_L	1.733	0.56
47_E	195_S	1.671	0.52
101_H	209_N	1.628	0.49
31_F	117_A	1.614	0.48
135_A	210_I	1.586	0.46
31_F	163_S	1.547	0.43
12_L	190_A	1.542	0.43
184_L	210_I	1.537	0.43
54_Q	69_L	1.519	0.42
137_G	174_I	1.506	0.41
36_L	167_L	1.475	0.39
113_E	156_S	1.460	0.38
24_I	206_Q	1.457	0.38
13_F	18_A	1.442	0.37
29_T	36_L	1.430	0.36
112_A	117_A	1.410	0.35
159_S	163_S	1.408	0.35
13_F	126_M	1.399	0.34
100_I	127_H	1.394	0.34
135_A	167_L	1.324	0.30
57_Y	208_G	1.324	0.30
133_N	145_N	1.319	0.30
76_P	103_G	1.304	0.29
89_L	101_H	1.296	0.28
30_D	192_L	1.289	0.28
83_L	162_G	1.272	0.27
38_P	116_P	1.261	0.26
59_L	173_D	1.260	0.26
134_A	138_T	1.252	0.26
115_Y	125_Y	1.252	0.26
79_F	183_W	1.249	0.26
129_Q	148_E	1.232	0.25
90_S	206_Q	1.228	0.25
27_I	121_N	1.225	0.25
121_N	156_S	1.224	0.25
18_A	126_M	1.223	0.25
73_I	115_Y	1.222	0.24
60_A	210_I	1.219	0.24
121_N	213_D	1.212	0.24
90_S	159_S	1.208	0.24
50_L	80_T	1.206	0.24
150_A	196_L	1.204	0.24
16_N	61_Q	1.196	0.23
87_S	166_D	1.170	0.22
106_T	213_D	1.166	0.22
200_D	213_D	1.160	0.22
30_D	106_T	1.143	0.21
34_R	162_G	1.140	0.21
187_A	210_I	1.133	0.20
134_A	170_R	1.129	0.20
28_Q	151_I	1.126	0.20
60_A	107_Y	1.111	0.19
34_R	53_I	1.109	0.19
98_G	162_G	1.109	0.19
154_L	183_W	1.107	0.19
81_R	134_A	1.106	0.19
66_K	69_L	1.104	0.19
97_S	175_Y	1.099	0.19
3_P	50_L	1.095	0.19
51_K	172_G	1.092	0.19
129_Q	158_A	1.092	0.19
22_Y	107_Y	1.090	0.19
50_L	76_P	1.089	0.19
19_T	90_S	1.088	0.18
147_G	174_I	1.087	0.18
153_A	193_S	1.086	0.18
148_E	153_A	1.082	0.18
187_A	197_L	1.082	0.18
109_F	172_G	1.080	0.18
109_F	137_G	1.079	0.18
154_L	206_Q	1.075	0.18
159_S	187_A	1.074	0.18
2_L	110_R	1.073	0.18
17_S	53_I	1.072	0.18
150_A	177_L	1.071	0.18
113_E	201_N	1.071	0.18
135_A	184_L	1.069	0.18
71_P	140_L	1.069	0.18
167_L	199_A	1.067	0.18
162_G	187_A	1.063	0.18
165_S	188_N	1.063	0.18
135_A	149_D	1.061	0.17
195_S	198_S	1.056	0.17
64_T	138_T	1.055	0.17
83_L	159_S	1.055	0.17
172_G	176_Y	1.052	0.17
71_P	122_L	1.052	0.17
173_D	204_F	1.051	0.17
115_Y	177_L	1.050	0.17
55_L	86_G	1.048	0.17
9_F	122_L	1.043	0.17
79_F	154_L	1.041	0.17
12_L	193_S	1.041	0.17
82_S	106_T	1.037	0.17
36_L	132_P	1.036	0.16
50_L	103_G	1.036	0.16
132_P	200_D	1.036	0.16
82_S	141_Y	1.034	0.16
107_Y	173_D	1.034	0.16
137_G	167_L	1.033	0.16
29_T	129_Q	1.028	0.16
4_E	85_K	1.028	0.16
14_D	187_A	1.027	0.16
42_L	45_T	1.027	0.16
99_L	169_L	1.024	0.16
8_L	58_K	1.023	0.16
40_S	59_L	1.022	0.16
24_I	85_K	1.020	0.16
155_V	205_I	1.018	0.16
89_L	107_Y	1.014	0.16
78_V	103_G	1.013	0.16
19_T	60_A	1.012	0.16
19_T	55_L	1.011	0.16
9_F	126_M	1.010	0.16
82_S	194_Y	1.010	0.16
42_L	146_M	1.005	0.15
15_Y	165_S	1.003	0.15

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
3f0iA	2	0.514	26.8	0.966	Contact Map
3rdwA	2	0.4953	18.2	0.968	Contact Map
1pbuA	1	0.6449	11.7	0.971	Contact Map
3fz4A	1	0.5047	9.5	0.972	Contact Map
1y0nA	1	0.1776	7.2	0.974	Contact Map
1avoA	7	0.257	5.6	0.975	Contact Map
3gkxA	2	0.5093	5.5	0.975	Contact Map
3hshA	6	0.257	5.4	0.975	Contact Map
3d3aA	1	0.2664	4.9	0.975	Contact Map
3n3fA	2	0.2477	4.9	0.976	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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