OPENSEQ.org - 1441331436 - GREMLIN Submission

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Tcb2

ID:	1441331436	Query Sequence MAQYSQTLRSSGFTSTVGLTDIEGAKTVARRIFENYDKGRKGRIENTDCVPMITEAYKSFNSFFAPSSDDIKAYHRVLDRNGDGIVTYQDIEELCIRYLTGTTVQRTIVTEEKVKKSSKPKYNPEVEAKLDVARRLFKRYDKDGSGQLQDDEIAGLLKDTYAEMGMSNFTPTKEDVKIWLQMADTNSDGSVSLEEYEDLIIKSLQKAGIRVEKQSLVF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	218 (191)
Sequences:	255 (193)
Seq/Len:	1.335
Nf(neff/√len):	14.0

HHblits Results: (2015_06)
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: 1.335).

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
39_G	48_D	3.057	1.00
152_E	188_D	2.929	1.00
184_D	189_G	2.472	1.00
184_D	195_E	2.384	0.99
152_E	195_E	2.354	0.99
83_D	188_D	2.107	0.98
48_D	90_D	2.063	0.98
141_D	146_G	2.034	0.98
188_D	195_E	2.022	0.98
41_K	48_D	2.009	0.98
37_D	48_D	1.927	0.97
152_E	184_D	1.849	0.95
53_I	157_L	1.811	0.95
141_D	184_D	1.777	0.94
152_E	186_N	1.750	0.93
183_A	200_I	1.619	0.89
83_D	90_D	1.613	0.89
33_F	37_D	1.590	0.88
44_I	180_L	1.569	0.87
79_D	84_G	1.531	0.85
144_G	157_L	1.475	0.82
83_D	87_T	1.457	0.81
143_D	195_E	1.380	0.76
90_D	195_E	1.376	0.76
79_D	90_D	1.350	0.74
184_D	188_D	1.324	0.72
79_D	83_D	1.320	0.71
79_D	195_E	1.315	0.71
153_I	171_P	1.305	0.70
37_D	141_D	1.300	0.70
36_Y	140_Y	1.296	0.69
49_C	149_Q	1.291	0.69
93_E	198_D	1.290	0.69
48_D	184_D	1.289	0.69
176_V	191_V	1.280	0.68
33_F	88_Y	1.256	0.66
33_F	91_I	1.256	0.66
32_I	190_S	1.240	0.64
137_F	184_D	1.230	0.64
74_Y	196_Y	1.213	0.62
189_G	195_E	1.210	0.62
81_N	90_D	1.203	0.61
88_Y	193_L	1.200	0.61
48_D	152_E	1.194	0.60
52_M	156_L	1.193	0.60
83_D	152_E	1.160	0.57
79_D	193_L	1.159	0.57
107_T	173_K	1.158	0.57
33_F	146_G	1.157	0.57
143_D	189_G	1.151	0.56
147_Q	157_L	1.142	0.55
24_G	157_L	1.136	0.54
99_L	191_V	1.132	0.54
37_D	44_I	1.132	0.54
37_D	184_D	1.131	0.54
92_E	139_R	1.131	0.54
138_K	148_L	1.120	0.53
75_H	191_V	1.116	0.52
33_F	70_D	1.111	0.52
153_I	179_W	1.109	0.52
48_D	81_N	1.101	0.51
37_D	42_G	1.100	0.51
90_D	152_E	1.089	0.50
145_S	152_E	1.088	0.50
49_C	53_I	1.086	0.49
53_I	81_N	1.085	0.49
32_I	95_C	1.080	0.49
44_I	96_I	1.077	0.49
61_N	148_L	1.076	0.48
152_E	189_G	1.073	0.48
77_V	140_Y	1.072	0.48
45_E	79_D	1.068	0.48
45_E	127_E	1.066	0.47
72_K	150_D	1.059	0.47
148_L	201_I	1.056	0.46
198_D	201_I	1.052	0.46
106_R	143_D	1.050	0.46
87_T	186_N	1.047	0.46
89_Q	111_E	1.022	0.43
71_I	95_C	1.017	0.43
131_D	148_L	1.012	0.42
70_D	199_L	1.009	0.42
37_D	137_F	1.007	0.42
67_S	109_V	1.006	0.42
126_V	130_L	1.005	0.41
74_Y	96_I	1.003	0.41
179_W	193_L	1.000	0.41

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
3mwuA	1	0.6881	99.9	0.493	Contact Map
4mvfA	1	0.7385	99.9	0.505	Contact Map
3u0kA	1	0.7156	99.9	0.507	Contact Map
3q5iA	1	0.7569	99.9	0.508	Contact Map
3nyvA	1	0.7569	99.9	0.509	Contact Map
4i2yA	2	0.7385	99.9	0.514	Contact Map
4qoxA	1	0.7798	99.9	0.514	Contact Map
1m45A	1	0.6514	99.9	0.518	Contact Map
3lijA	1	0.7569	99.9	0.518	Contact Map
4c0kA	1	0.8532	99.9	0.519	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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